Highlighting vs. Track Changes

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-28

Quick Answer

• Use track changes when the editor or journal requires a visible revision history, and use highlighting when you need to draw attention to specific text within an otherwise clean document.
• Check the journal's author guidelines before revising, because many journals specify which marking method they accept for revised manuscripts.
• Neither method replaces a separate response letter that lists each reviewer comment and explains how you addressed it.

What This Comparison Covers

Authors revising a manuscript face a practical decision about how to mark their changes. The choice between highlighting and track changes affects how editors, reviewers, and coauthors see your work. Each method has strengths and weaknesses that depend on the revision stage, the journal's requirements, and the preferences of your collaborators.

This article compares highlighting and track changes for manuscript revision. It explains how each method works, when to use one over the other, and how to combine them with a reviewer response letter. The guidance applies to students, researchers, laboratory staff, and life-science professionals preparing revised manuscripts for submission.

At a Glance

Core Principles of Manuscript Revision Marking

Why Marking Method Matters

Peer review depends on editors and reviewers being able to see what changed between versions. The Committee on Publication Ethics core practices describe the responsibilities of authors and editors during peer review. Transparent revision marking supports that process because it lets reviewers focus on the changes you made instead of rereading the entire manuscript.

The marking method you choose also affects how easily your co-authors can review your work. A postdoctoral fellow revising a paper with five co-authors needs a method that everyone can follow. A graduate student responding to a single reviewer may need a simpler approach.

The Role of the Response Letter

No marking method replaces a response letter. The response letter is where you list each reviewer comment and explain what you changed. The EQUATOR Network provides reporting guidelines that help authors structure their research reporting, and the same principle applies to revision responses. A clear response letter tells the editor and reviewers exactly where to look in the revised manuscript.

Your response letter should include the reviewer comment, your response, and the location of the change in the manuscript. This structure works with either highlighting or track changes.

Highlighting for Manuscript Revision

How Highlighting Works

Highlighting applies a colored background to selected text. The text itself remains unchanged. You can use different colors to distinguish types of changes, such as yellow for content changes and green for new references.

Highlighting is a formatting feature in most word processors. It does not record who made the change or when. It does not show deleted text. If you remove a sentence and do not highlight the deletion, the reviewer cannot see that the sentence was removed.

When Highlighting Is the Better Choice

Highlighting works well when you have a small number of targeted changes. For example, if a reviewer asked you to clarify one sentence in the methods section, highlighting that sentence makes it easy for the reviewer to find it.

Highlighting also works when you need to submit a clean manuscript. Some journals ask for a clean version with changes highlighted instead of a version with track changes. The clean version is easier to read, and the highlighting draws attention to the specific passages that changed.

Highlighting is useful when you want to preserve the original text and show the revised text in place. The reviewer sees the final wording with a visual marker that says this passage was changed.

Limitations of Highlighting

Highlighting does not show what the original text said. A reviewer who wants to compare the old and new wording must look at the previous version separately. This is a significant limitation when the change is substantial.

Highlighting can be lost during file conversion. If you convert your document to PDF, the highlighting usually remains visible. But if you copy text into another document or use an online submission system that processes the file, the highlighting may disappear.

Highlighting also does not track who made the change. If multiple co-authors revise the same document, you cannot tell who changed what. This matters in collaborative projects where authorship and responsibility are under discussion. The Committee on Publication Ethics core practices address authorship expectations, and clear attribution of changes supports that process.

Track Changes for Manuscript Revision

How Track Changes Works

Track changes records every insertion, deletion, and formatting change in the document. Each change is attributed to the author who made it, with a timestamp. The document shows the original text with strikethrough for deletions and underlined or colored text for insertions.

The editor or reviewer can accept or reject each change. This creates a permanent record of the revision process. The final version, after all changes are accepted, is a clean manuscript.

When Track Changes Is the Better Choice

Track changes works best for extensive revisions. If you rewrote a section, moved paragraphs, or made dozens of small edits, track changes gives the editor a complete picture of what you did.

Track changes is also the better choice when multiple co-authors are working on the same document. Each author's changes are attributed to them. This is important in collaborative projects where the final manuscript must reflect the contributions of all authors.

Track changes is useful when you need to show the editor exactly what you changed in response to a specific comment. The editor can see the original text and the new text side by side.

Limitations of Track Changes

Track changes can be overwhelming when the revisions are extensive. A manuscript with hundreds of tracked changes is difficult to read. The reviewer may struggle to see the final version of the text.

Track changes can also be missed if the file is converted. Some online submission systems do not display track changes correctly. The editor may see a clean version without realizing that changes were tracked.

You must accept or reject all changes before the final submission. If you forget to accept a change, the manuscript may contain both the old and new text. This is a common error that delays publication.

How to Choose Between Highlighting and Track Changes

Step 1: Check the Journal Guidelines

The journal's author guidelines are the first place to look. Many journals specify how they want revisions marked. Some ask for track changes. Some ask for a clean version with changes highlighted. Some ask for both.

If the guidelines are unclear, contact the editorial office. A short email asking about the preferred marking method can save you from resubmitting your manuscript.

Step 2: Assess the Scope of Your Revisions

Count the number of changes you made. If you have fewer than ten targeted changes, highlighting is often sufficient. If you have rewritten entire sections, track changes gives the editor a better picture of your work.

Step 3: Consider Your Co-Authors

If you are working with co-authors, ask them how they want to review the changes. Some prefer track changes because they can see the full history. Others prefer highlighting because the document is easier to read.

Step 4: Prepare the Response Letter

Regardless of the marking method, prepare a response letter that lists each reviewer comment and your response. The EQUATOR Network provides guidance on transparent reporting, and a clear response letter is part of that transparency.

Practical Workflow for Marking Revisions

Step 1: Save the Original Version

Before you start revising, save a copy of the original manuscript. This is your reference version. You will need it to compare your changes and to write your response letter.

Step 2: Make Your Changes

Make your changes in the manuscript. If you are using track changes, turn it on before you start. If you are using highlighting, make the changes first and then highlight the revised text.

Step 3: Review the Changes

Read through the revised manuscript and check that every change is marked. Look for text that you changed but did not highlight or track. Look for tracked changes that you intended to accept.

Step 4: Write the Response Letter

Write your response letter. List each reviewer comment and your response. Include the location of the change in the manuscript. This letter is your primary communication with the editor and reviewer.

Step 5: Convert and Check the File

Convert your manuscript to the format required by the journal. Check that the highlighting or track changes are visible in the converted file. If the conversion removes the markings, you need to fix the file before submission.

Records and Measurements

What to Record

Keep a record of your revision process. This includes the original version, the revised version, and the response letter. You should also record the date you submitted the revision and the date you received the decision.

How to Measure Your Progress

Track the number of changes you made and the number of reviewer comments you addressed. This helps you confirm that you have responded to every comment. A simple table with columns for comment number, your response, and the manuscript location is useful.

What to Keep for Your Records

Keep the original manuscript, the revised manuscript, and the response letter. These documents are part of your research record. The National Library of Medicine provides access to research-method references that emphasize the importance of maintaining accurate records.

Common Failure Patterns

Failure Pattern 1: Highlighting That Disappears

Authors sometimes submit a manuscript where the highlighting is not visible. This happens when the file is converted to PDF and the highlighting is not preserved, or when the author copies text from one document to another.

Prevention: Check the converted file before submission. Open the PDF and confirm that the highlighting is visible.

Failure Pattern 2: Track Changes That Are Not Accepted

Authors sometimes submit a manuscript with tracked changes that have not been accepted. The editor sees a clean version and does not realize that changes are pending.

Prevention: Accept all changes before submission. Then read the final version to confirm that it is clean.

Failure Pattern 3: The Response Letter Does Not Match the Changes

Authors sometimes write a response letter that describes changes that are not marked in the manuscript. The reviewer cannot find the change and the revision is rejected.

Prevention: Cross-check your response letter against the manuscript. Confirm that each change you describe is visible in the revised version.

Failure Pattern 4: The Wrong Version Is Submitted

Authors sometimes submit the original version instead of the revised version. This is a common error when multiple versions of the file exist.

Prevention: Name your files clearly. Use a version number and the date. Confirm that the file you are submitting is the correct one.

Welfare and Safety Context

Research Integrity and Peer Review

The Committee on Publication Ethics core practices describe the responsibilities of authors during peer review. Clear revision marking is part of that responsibility. When you mark your changes clearly, you help the editor and reviewer evaluate your work fairly.

Transparency in Research Reporting

The EQUATOR Network promotes transparent research reporting. A clear revision process supports transparency because it shows the editor and reviewer exactly what you changed and why.

Data Management and Sharing

The National Institutes of Health data management and sharing policy describes expectations for managing and sharing research data. Your revision records are part of your research data. Keeping them organized supports good data management.

Limitations and Professional Escalation

When to Ask for Help

If you are unsure about the marking method, ask the journal editorial office. They can tell you what they expect. If you are working with co-authors, ask them how they want to review the changes.

When to Escalate

If you cannot resolve a disagreement with a co-author about the marking method, escalate the issue to the corresponding author or the principal investigator. If you believe the journal's requirements are unclear, contact the editorial office directly.

When to Seek Professional Advice

If you are preparing a manuscript for a journal with specific formatting requirements, consider consulting a professional editing service. They can help you format your revision correctly.

A Decision Framework for Mixed Revision Scenarios

When One Method Is Not Enough

The choice between highlighting and track changes is rarely a single decision. Many revised manuscripts contain different types of changes that benefit from different marking approaches. A revision that adds a new statistical analysis, rewrites the discussion, and corrects a typo in the abstract presents three distinct marking needs. Treating the entire manuscript as one unit forces you to choose a single method that may serve one type of change well and another poorly.

A practical decision framework separates your revisions into categories and applies the appropriate marking method to each. This approach preserves the strengths of both highlighting and track changes while avoiding their individual weaknesses. The framework works because it matches the marking method to the nature of the change instead of applying one method uniformly.

Categorize Your Revisions Before You Mark

Start by listing every change you made during the revision. Work through the reviewer comments and your own edits. Assign each change to one of three categories.

The first category is substantive content changes. These are rewrites, new paragraphs, moved sections, replaced analyses, or altered interpretations. A reviewer asked you to reinterpret your results or you added a new limitations paragraph. These changes alter the meaning of the manuscript. The editor and reviewer need to see both the original wording and the new wording to evaluate whether you addressed the comment adequately.

The second category is targeted clarifications. These are single sentences or short passages where you refined wording without changing the underlying meaning. You clarified a method step, corrected a term, or tightened a vague phrase. The reviewer needs to find these passages quickly, but does not need a full history of the original wording.

The third category is formatting and minor corrections. These are typo fixes, reference updates, punctuation changes, and formatting adjustments. These changes do not affect the scientific content and rarely need to be shown to the reviewer at all.

Apply the Matching Marking Method

For substantive content changes, use track changes. The editor needs to see the original text and the replacement text to judge whether your revision responds to the reviewer comment. Track changes preserves both versions in place. The Committee on Publication Ethics core practices describe the expectation that authors respond transparently to peer review. Showing the full history of substantive changes supports that transparency because the editor can verify exactly what you altered.

For targeted clarifications, use highlighting. These changes are small enough that the reviewer can read the final wording directly. Highlighting draws attention to the specific passage without cluttering the document with strikethrough text. The reviewer sees the clarified sentence and can evaluate it immediately. This works well when the change is self-explanatory and the original wording is not needed for comparison.

For formatting and minor corrections, make the change without marking it. A typo fix or reference update does not need to be shown to the reviewer. Marking these changes adds noise to the document and distracts from the substantive revisions. The response letter can note that you corrected typographical errors without listing each one.

Document the Framework in Your Response Letter

The response letter becomes the map that ties the marking methods together. For each reviewer comment, state which marking method you used for the corresponding change. Write something like this: the revised paragraph in the methods section appears with track changes, and the clarified sentence in the discussion is highlighted in yellow. This tells the reviewer exactly what to look for and where.

The EQUATOR Network provides reporting guidelines that emphasize clear and transparent research reporting. A response letter that explains your marking system is part of that transparency. The reviewer does not have to guess whether a highlighted passage is a new addition or a clarification of existing text.

A Worked Example of the Framework

Consider a revision responding to three reviewer comments. Comment one asks you to add a sensitivity analysis to the results section. Comment two asks you to clarify how you handled missing data in the methods section. Comment three asks you to correct a citation error in the references.

Under the framework, you add the sensitivity analysis with track changes. The editor sees the new paragraph and can compare it with the surrounding text. You clarify the missing data sentence with highlighting. The reviewer sees the final wording with a visual marker. You correct the citation without marking it. The response letter explains each choice.

This mixed approach gives the editor a clear view of the substantive addition, gives the reviewer a clean read of the clarification, and avoids cluttering the document with a tracked typo fix. Each marking method serves the type of change it handles best.

When the Mixed Framework Does Not Work

The framework assumes the journal accepts both marking methods in the same manuscript. Some journals require a single method for the entire document. If the author guidelines specify track changes only or highlighting only, follow the journal requirement and apply that method to all changes.

The framework also assumes your co-authors can follow a mixed system. If a co-author is unfamiliar with track changes or finds the combination confusing, simplify the approach. The goal is a revision that the editor and reviewers can evaluate, not a demonstration of marking sophistication.

Troubleshooting the Mixed Framework

The most common problem with the mixed framework is losing track of which changes are marked with which method. A change that should be highlighted is tracked instead, or a substantive change is only highlighted without showing the original wording.

Prevent this by creating a revision log before you start marking. List each change, assign it to a category, and note the marking method. Use a simple table with columns for the change location, the category, and the marking method. Check each change against the log after you finish marking.

Another common problem is that highlighting and track changes interact poorly in the same document. If you highlight text that also contains tracked changes, the reviewer may see a highlighted passage with strikethrough text inside it. This happens when you highlight a passage and then edit it with track changes enabled. Avoid this by deciding the marking method for each passage before you edit it.

Records for the Mixed Framework

Keep the revision log with your other revision records. The National Library of Medicine provides access to research-method references that emphasize maintaining accurate records throughout the research process. The revision log documents your marking decisions and helps you verify that every reviewer comment is addressed.

Store the original version, the revised version with mixed markings, and a clean version with all changes accepted. The clean version is useful if the journal asks for a final manuscript without markings. The National Institutes of Health data management and sharing policy describes expectations for managing research records. Your revision files are part of that record.

Professional Escalation for Marking Conflicts

If a journal requires a marking method that conflicts with your framework, follow the journal requirement. If the journal guidelines are unclear about whether mixed marking is acceptable, contact the editorial office before submission. A brief email asking whether you may use track changes for substantive revisions and highlighting for clarifications can prevent a returned manuscript.

If a co-author disagrees with the mixed framework, explain the reasoning behind it. Show the revision log and how each change is categorized. If the disagreement continues, escalate to the corresponding author or principal investigator. The Committee on Publication Ethics core practices describe the expectation that co-authors resolve disputes through appropriate channels.

When to Use the Framework Versus a Single Method

Use the mixed framework when your revision contains changes of different types and the journal does not require a single method. Use a single method when the journal specifies one, when your revision is uniformly substantive or uniformly minor, or when your co-authors prefer one approach.

A revision that only adds new analyses and rewrites sections benefits from track changes throughout. A revision that only clarifies a few sentences benefits from highlighting throughout. The mixed framework is for the common situation where your revision includes both types of changes and you want each one marked in the way that serves the reviewer best.

Frequently Asked Questions

Should I use highlighting or track changes for a minor revision?

For a minor revision with a small number of changes, highlighting is often sufficient. It keeps the document clean and draws attention to the specific passages you changed. Check the journal guidelines first, because some journals require track changes.

Can I use both highlighting and track changes in the same manuscript?

You can use both, but it is usually unnecessary. Using both can confuse the reviewer because the document becomes cluttered. Choose one method and use it consistently.

How do I know which method the journal requires?

Read the journal's author guidelines. If the guidelines do not specify, contact the editorial office and ask. A short email can save you from resubmitting your manuscript.

What is the difference between highlighting and track changes?

Highlighting adds a colored background to text without changing the text itself. Track changes records every insertion and deletion, showing the original text and the new text. Track changes also attributes each change to the author who made it.

Do I still need a response letter if I use track changes?

Yes. The response letter is separate from the marking method. It lists each reviewer comment and your response. The response letter is the primary way you communicate with the editor and reviewer.

What happens if the journal does not accept my marking method?

The journal may return your manuscript for revision. You will need to reformat the manuscript using the method the journal requires. This is why it is important to check the guidelines before you submit.

How do I make sure my highlighting or track changes are visible in the PDF?

After converting your file to PDF, open the PDF and check that the markings are visible. If the highlighting or track changes are not visible, you need to fix the file before submission.

What should I do if I accidentally submit the wrong version?

Contact the editorial office immediately. Explain the error and submit the correct version. Most journals will accept a corrected submission if you act quickly.

Using the Evidence

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• Sample Size Symbol and Notation: What You Need to Know

References and Further Reading

• Research Methods Resources. National Library of Medicine.
• EQUATOR Network. EQUATOR Network.
• Core Practices. Committee on Publication Ethics.
• NIH Grants and Funding. National Institutes of Health.
• ORCID for Researchers. ORCID.
• Data Management and Sharing Policy. National Institutes of Health.
• NCBI Literature Resources. National Center for Biotechnology Information.
• PubMed. National Library of Medicine.

This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.