How to Compare Documents With AI (Side by Side, With Citations)

To compare documents with AI, you load more than one file into the same project and ask a question that spans both, instead of opening two tabs and eyeballing them side by side. “What changed between draft 1 and draft 2 of this contract?” or “Where do these two papers disagree on methodology?” gets answered by pulling the relevant passage from each source and pointing back to where it found it.

Under the hood it works the same way as any other document Q&A: each file is split into chunks, embedded, and retrieved by relevance to your question — see our RAG explainer for the mechanism. Comparison isn't a special mode; it's the same retrieval pulling from two sources instead of one, so the answer can cite either file for any claim it makes.

1. Create a project (or reuse one) and upload every document you want to compare — PDFs, contracts, drafts, papers, or slide decks.
2. Wait for every file to finish indexing before asking a comparison question, so the answer can actually draw on all of them.
3. Ask directly: “Compare X and Y on [a specific point]” rather than requesting one summary at a time.
4. Check the citation on each side of the comparison — a real difference should point to a specific passage in each file, not just one.
5. Narrow further with follow-ups: “Which one specifies a longer notice period?” or “Does either mention a renewal clause?”

Asking for a summary of each document separately and reading them next to each other feels like comparing, but it puts the synthesis work on you — you still have to notice what's missing from one and present in the other. A direct comparison question does that matching for you: it looks for the corresponding point in both sources and reports the difference (or confirms there isn't one), with a citation on each side you can check. That's the difference between two separate summaries and an actual comparison.

Comparison only works if both documents live in the same project — if one sits in an old project and you upload the other into a brand-new one, there's no single question that can see both. This is one of the clearest cases for organizing documents into projects by topic: group everything you might ever want to compare in one place from the start, rather than discovering later that your two contract drafts live in different notebooks. It's the same principle behind querying a whole library at once instead of one file at a time — see what to look for in an AI research assistant for more on multi-source projects.

Doxy lets you run document Q&A across every file in a project at once, so comparing two contract drafts, two research papers, or a syllabus against a textbook chapter is just a differently-worded question — not a separate feature. Upload both files, wait for them to index, and ask what's different.