When you get abducted by Voldemort, he requires genealogy records, and blood tests to be taken. She expected hers to come back as a dirty mudblood, but it didn't. It turns out, Voldemort had a wife and was expecting a child. Dumbledore and a few other Order members attacked and captured his wife, Marielle. They must have held her captive until she gave birth before they killed her, leaving her very pregnant looking body for Voldemort to find. After he dropped that bombshell, he removed a very powerful and well-hidden glamour charm from Hermione. She saw what she truly looked like for the first time, and loved it.