The default for most PDF objects is knockout. If you place a red circle on top of a blue rectangle, the press prints the blue rectangle with a circle-shaped hole in it, then prints the red circle to fill the hole. Each ink lives in its own area.
Knockout is usually correct. It means the color you see on screen is the color that will print.
Overprint is the opposite. The top object prints over the ink beneath. If that red circle had overprint on, the press would print the full blue rectangle, then print the red circle on top, and where they overlap, the result is a mixture of both inks (on coated paper, probably a dark muddy purple).
Black text on colored backgrounds. Any body copy set in 100% K should overprint. If the K text knocks out the color beneath, any registration drift between the black plate and the color plates produces a visible fringe. You can see the colored edge peeking around the letters. Overprint black sits on top of the color, so drift becomes invisible. RIPs often apply this automatically (called "overprint black" or "overprint preservation"), but it's safer to set it explicitly in the file.
Trapping. On fast-running flexo and offset presses, adjacent colors that meet at an edge can register imperfectly. Tiny white gaps appear between them. Trapping intentionally overlaps the two colors at the border (the lighter color extends into the darker one) so any misregistration is absorbed. The overlap is implemented using overprint.
Spot varnishes and foil. A gloss spot varnish always overprints the color below, the varnish is a clear coating meant to sit on top of existing artwork, not replace it.
Colored fills with overprint left on by mistake. A yellow shape with overprint on, placed over a blue background, becomes green on press. The designer sees yellow on screen, but the press adds yellow on top of the blue and the result is a muddy green. Always unless there's a specific reason for it, colored fills should knock out.
Overprinted 0% fills. Sometimes a shape is filled with 0% of a color (invisible) but overprint is set. The result looks blank on screen but causes a real knockout on press (or no effect at all), depending on the RIP. Either way, unpredictable.
Illustrator: Select any object, then Window → Attributes. The Attributes panel shows "Overprint Fill" and "Overprint Stroke" checkboxes. If either is checked, that object overprints.
InDesign: Same. Window → Output → Attributes. Overprint Fill/Stroke checkboxes.
Acrobat Pro: View → Tools → Print Production → Output Preview. Turn on "Simulate Overprinting" to see exactly what will print. This is the gold-standard preview. It shows what the press will actually do, not just what the screen displays.
Preflight tools: Automated preflight scans every object and reports which ones overprint. Flags to watch for: "white ink overprinting" (almost always a bug), "non-black ink overprinting" (usually a bug unless intentional trapping), "light color over dark color knockout" (usually correct but worth verifying).
Preflight scans every object for overprint attributes, flags white ink set to overprint, and catches the classic traps before your file hits the RIP.
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