PDF Opening Issues

Fix Incorrect PDF Structure Error When Comparing Files

Rana Garcia Oct 28, 2026 869 views

Question details

The user is unable to compare two PDF files because the application throws an error regarding the internal structure of the document.

Fix Incorrect PDF Structure Error When Comparing Files

Product: Adobe Acrobat
Device & OS: not provided
Scenario: Attempting to use the Compare Files feature to find differences between two versions of a PDF document.
Observed behavior: The application fails to complete the comparison and displays the message: "An incorrect structure was found in the PDF file."

Before you start

Verify whether the error is isolated to a specific PDF by testing the 'Compare Files' feature with two completely different, known-working PDF documents.

Solution 1Recommended

Open and Resave the PDF File

Resaving the PDF in your current application can automatically rewrite the code and repair minor structural corruptions.

PDF files can sometimes accumulate hidden structural errors if they are repeatedly edited or exported from non-standard third-party tools. Simply opening and saving a new copy forces the PDF software to rebuild the file's internal structure.

Open the Problematic PDF

Launch your PDF application and open the specific file that is causing the comparison error.

Save as a New File

Navigate to 'File' in the top menu, select 'Save As', and save the document with a new name to a local folder on your computer.

Retry the Comparison

Open the 'Compare Files' tool again and select your newly saved PDF file to see if the structure error is resolved.

Tip: If you are unsure which of the two files is causing the error, perform the 'Save As' process on both documents before comparing.

Solution 2

Recreate the PDF from the Source Document

If resaving does not resolve the structural issue, recreating the file from the original Word or Excel document ensures a clean PDF structure.

Compare PDFs Seamlessly

Easily Compare PDF Files with WPS Office

If your current PDF software struggles with structural errors, try using WPS Office. The built-in WPS PDF tool offers a lightweight, highly compatible, and fast file comparison feature that effortlessly highlights differences without getting bogged down by minor structural syntax issues.

1. Open WPS PDF: Download and launch WPS Office, then switch to the 'PDF' tab on the home screen.
2. Access the Compare Tool: Navigate to the 'Tools' menu at the top and click on the 'Compare PDF' feature.
3. Upload Your Files: Select the original PDF document and the revised version you wish to check.
4. Run the Comparison: Click the 'Compare' button. WPS PDF will smoothly process the files and generate a side-by-side view highlighting all modifications.

Reliable PDF comparison tool that quickly identifies text and layout differencesHighly compatible with all standard PDF versions and Microsoft Office formatsLightweight application that runs smoothly on everyday devicesComprehensive PDF toolkit for editing, merging, and converting files

Frequently Asked Questions

Why does a PDF get an 'incorrect structure' error?

This error generally occurs when a PDF is generated by a non-standard application, interrupted during the saving process, or heavily edited over time, causing its internal syntax or tagging structure to become corrupted.

Can I compare scanned PDFs that contain no selectable text?

To compare scanned PDFs effectively, you must first run an OCR (Optical Character Recognition) tool to convert the image-based document into searchable and selectable text. Once recognized, the comparison tool can identify changes.

Is it possible to check a PDF for structural errors before comparing?

Yes, advanced PDF editors often feature a 'Preflight' tool located in the print production or optimization settings. Running a Preflight check can identify and automatically fix syntax or structural anomalies within the file.

PDF Troubleshooting