Nicole Kidman has secretly kept DNA samples from the baby she miscarried — which she says can prove that her estranged husband Tom Cruise is the father of the child, THE ENQUIRER has learned exclusively.

The issue that hits stands Friday reveals that Nicole is terrified Tom might make allegations of unfaithfulness against her and deny he was the father. And she believes that if she could prove to Tom that he was the father, he’d take her back, sources say.

The ENQUIRER exclusive also details Nicole’s desperate attempt to save the marriage … how Tom refused even to talk with her after the miscarriage … why Sly Stallone told Nicole’s orthopedic surgeon to stop seeing her … and much more.