Rohman
You spent an hour highlighting the contract and writing margin comments. The other side opened it and saw a clean document. Or your notes made it to their screen and not to their printer. Nobody deleted anything. When you annotate a PDF, your markups live on a separate layer from the page, and that layer is optional equipment in every viewer and every print dialog.
If you just want the short version: open the file, pick a highlight or note tool, mark it up, download. Four steps. What's worth reading is what happens after step four, because that's where most annotation workflows quietly fall apart.
- Open the PDF in OxygenPDF's annotate tool. Nothing uploads; it opens straight in your browser tab.
- Pick a tool: highlight, underline, strikethrough, sticky note, callout, arrow, shape, stamp, or freehand pen.
- Mark it up. Text-anchored tools (highlight, underline, strikethrough) snap to whatever you've selected on the page; freeform tools go wherever you drag them.
- Download. Everything you just drew gets baked directly into the page, not left on a layer a future viewer can choose to skip. One tool is the exception; it's covered further down.
That fourth step is this article's actual subject. A PDF page is two documents stacked. The content stream holds the page itself: the text and images the author shipped. Annotations sit in a separate list attached to the page (the spec calls it /Annots) as objects overlaid on top. A highlight is a set of quadrilaterals hugging each line of selected text, and a pen stroke is an /Ink object tracing your hand. A sticky note is an icon whose comment text lives in metadata behind it. None of that touches the page underneath, which is exactly the point: markups can be moved, restyled, hidden, or deleted. It's also the whole problem.
Where Markups Go to Die
Every viewer implements the annotation layer differently, and some barely implement it at all.
Preview, Acrobat, and Apps That Don't Read Each Other's Annotations
The canonical casualty report comes from Apple's own support community: a user who added arrows, lines, and textboxes to a PDF in Preview found none of it survived being placed into Pages, InDesign, or Illustrator. Only their signature carried over. A veteran community member explained why in the same thread: "Apple's Preview is based on a substantially older PDF code base... [Adobe Reader and Preview] write annotations [in] different locations within the PDF" (Apple Support Community, thread 256271825). Two applications, two spec-compliant ways of writing the same /Annots array, and a third application that only ever reads one of them.
The Print Dialog's Silent Setting
Printing has its own trapdoor. Acrobat's print dialog has a Comments & Forms dropdown that defaults to "Document," which, per Adobe's own instructions, "prints the document contents and form fields, but not comments." You have to switch it to "Document and Markups" to get highlights and sticky notes onto paper at all (Adobe, Print comments), and the setting is sticky across sessions. A recipient who last printed a clean copy of something else will silently drop every highlight and comment you left, with nothing in the dialog telling them anything was skipped.
Browsers Were Viewers Only, for a Long Time
Browsers trained a generation into the same trap by being viewers only. Chrome's own PDF viewer, as opposed to the separate annotation tool ChromeOS's file app has carried for years, didn't get native markup until Chrome 145, in February 2026: highlighting, margin notes, and quick signatures, landing as what one outlet called "a top-requested Chrome feature, already available in Microsoft Edge and other browsers for some time" (9to5Google; Winbuzzer). For every version before that, which is still a meaningful share of the web given how gradually major-version rollouts reach everyone, "annotate in the browser" meant a print-to-PDF workaround that flattened the file and destroyed its searchable text on the way through.
A Black Highlight Is Not Redaction
And a warning that belongs in every markup guide: a black highlight is not redaction. The text underneath a dark annotation is still fully present in the file, one select-all away from exposure. If you're hiding something rather than emphasizing it, redact it properly instead.
| Scenario | What's actually at risk | Why |
|---|---|---|
| PDF placed into Pages, InDesign, or Illustrator | Arrows, lines, textboxes | The placing app reads the page's content, largely ignoring the annotation objects layered on top |
| Printed with Acrobat's dropdown left on "Document" | Every highlight and comment | The setting persists silently across sessions |
| Opened in Chrome before version 145 (pre-February 2026) | All of it | The built-in viewer only rendered pages; it didn't write or display annotations |
| A dark rectangle drawn "over" sensitive text | Nothing is actually hidden | The rectangle is a separate object; the text underneath is unchanged |
What's Actually in an /Annots Array
The vocabulary here is standardized, not tool-specific. ISO 32000-2, the current PDF specification, defines a fixed set of annotation subtypes, among them Text (the sticky-note icon), Highlight, Underline, StrikeOut, Line, Square, Circle, Ink, FreeText, and Stamp, each with its own required fields for position, color, opacity, and whatever text or appearance it carries (PDF Association, ISO 32000-2). Every PDF editor implements some subset of that list. The practical differences between tools are mostly about which subset they cover, and whether the tool bakes the mark into the page or leaves it standing as a separate object.
OxygenPDF's annotate tool covers highlight, underline, strikethrough, freehand pen and highlighter, sticky notes, callouts with a leader line pointing at what they're commenting on, arrows, shapes, and stamps. Each has a keyboard shortcut (H for the area highlighter, N for a sticky note, F for the freehand highlighter, and so on), so a long annotation pass doesn't mean reaching for the mouse between every mark. The full PDF editor adds whiteout, text boxes, and image insertion on top of that. Those change or cover the document rather than comment on it, which is the line the dedicated annotate page draws before leaving them out.
Annotating a Scanned PDF
Text-anchored highlighting needs something to anchor to: a real, selectable text layer. A scanned page, a photograph or fax with no OCR run over it, has none. That's why the annotate tool's default highlighter drags a translucent rectangle over whatever area you select, rather than snapping to text. That distinction matters in practice: open a scan and reach for a text-anchored highlight expecting it to hug a sentence, and it will silently do nothing, because there's no text there to hug. The area highlighter works on any page, scanned or not, precisely because it doesn't depend on one. If you need the words themselves to be selectable and searchable, not just visually marked, OCR the file before you start annotating it.
The Going Rates for a Highlighter
| Option | Cost | Where your file goes |
|---|---|---|
| Adobe Acrobat Reader (free tier) | Free, commenting and sticky notes included | Stays on your device (desktop or mobile app) |
| Adobe Acrobat Standard | $14.99/month, billed annually (Adobe pricing) | Your device, with optional cloud sync |
| Drawboard | Originally a one-time purchase (around $10); subscription-only today | Your device |
| Free browser-based annotators | Free | Uploaded to their server first; retention policy varies by tool |
| OxygenPDF | Free | Never leaves your browser |
Adobe's free Reader tier does cover commenting: highlights, sticky notes, drawing, with an upgrade prompt waiting the moment you need anything more, starting at $14.99 a month for Standard. Drawboard, long the pen-first favorite on Windows tablets, converted a one-time Microsoft Store purchase into an annual subscription; a Microsoft Q&A thread carries a user protesting they'd paid "10€" for what the store listing had promised was theirs "to own forever" (Microsoft Q&A), and Drawboard's own Trustpilot page has the reviews that followed (Trustpilot). And the free online annotators take the document itself as payment: upload-based tools hold your file on their servers. The honest ones keep it for an hour or two. Account storage keeps it indefinitely.
Think about what a marked-up document actually is. The base file might be a public form. Your annotations are the negotiation position, the diagnosis note, the grade, the feedback on the unreleased design. Uploading a markup session hands over the most sensitive layer of the document to a server you don't control.
Markups That Survive Every Viewer
OxygenPDF's annotate tool runs that whole vocabulary in your browser with nothing uploaded, and the full editor adds whiteout, text boxes, and image insertion for when marking up isn't enough. Both handle a password-protected file the same way every tool on this site does. Unlock it once with the password, and everything downstream, including export, works normally from there.
The export behavior is the part that actually answers this article's title. Highlight, underline, strikethrough, pen and freehand strokes, shapes, arrows, stamps, and callouts are all drawn directly into the page's content stream when you download: baked in, not layered on. They can't vanish in Preview, can't evaporate when the file is placed into a layout app, can't be dropped by a "Document"-mode printout, and can't be stripped by the recipient in two clicks.
Sticky notes are the one exception, and it's worth knowing why. They're saved the way the PDF spec expects a comment icon to work, as a real annotation object rather than page content, so hovering over one shows your note in any conforming reader. It also means the editor reads pre-existing sticky notes back in when you reopen a file, whichever app originally added them. That's the exact failure mode covered above, so if a note is bound for a layout tool that ignores the annotation layer entirely, use a callout instead of a sticky note for that one; a callout is drawn into the page like everything else on the list above. Either way, that permanence is a decision, so make it deliberately: keep your original file around if you'll want an unmarked copy later.
The inverse operation exists too. When someone sends you a PDF wearing a layer of stale comments, remove the annotations to strip /Annots clean; the page content underneath is untouched.
FAQ
Does highlighting a PDF change the text underneath?
No. A highlight, whether text-anchored or a drawn rectangle, is a separate object placed over the page. Select-all or copy-paste still pulls the original text unchanged, which is exactly why a highlight is not a substitute for redaction.
Why do my PDF comments disappear when I print?
Almost always because the print dialog's Comments & Forms dropdown is set to "Document" instead of "Document and Markups." The setting persists across sessions, so a document that printed clean last time prints clean again this time, with nothing warning you anything was left out.
Does a black highlight or shape actually hide the text under it?
Visually, yes; in the file, no. The mark lives in the annotation layer — the /Annots array this article is about — while the characters stay in the page's content stream, so select-all or any text extractor pulls them straight back out. Real redaction rewrites the page itself, which is a different job for a dedicated redaction tool.
Will annotations already in a file show up if I open it in OxygenPDF?
Sticky notes will. The editor recognizes native PDF Text annotations and loads them as editable objects no matter which app created them. The page content itself displays normally regardless, including anything another tool already baked into it.
Do PDF annotations work on scanned documents?
Freeform tools (the area highlighter, pen, shapes, stamps) work on any page. Text-anchored highlighting, underline, and strikethrough need a real text layer to snap to, which a scan doesn't have until it's been through OCR.
Does adding annotations affect a digitally signed PDF?
It can. A digital signature is computed over the file's exact byte range at signing time, and any later change, including adding a comment, can invalidate it in the signer's own software. Signers run into this often enough that it's a recurring thread in Adobe's own user community (Adobe Community). Finish marking up a document before anyone signs it, not after.
How do I remove someone else's annotations without touching the page?
Strip the annotation layer instead of editing the page. It clears everything in /Annots (highlights, notes, stamps, drawn shapes) and leaves the original content underneath untouched.
The Layer That Doesn't Disappear
Students marking lecture slides, teachers grading submissions, lawyers redlining drafts, designers stamping proof corrections: these workflows all eventually hit the moment where the markup has to survive a viewer nobody tested it against. Annotate the PDF in your browser, export it, and stop wondering which layer the other person will see. There's only one.
