All males who were present at the Fénélon-Notre Dame private school on 30 September 2013 were summoned to report at 8.00am on Monday so that plainclothes police could take swabs of their saliva to be tested.
The police have failed so far to find the man who raped a 16-year-old student in the toilets on that day.
The lights were off and the victim was unable to identify her assailant but a trace of his DNA was found.
So they hope to test the DNA of the 475 male pupils, 31 male teachers and 21 other employees or visitors present at the time.
The test cannot be carried out without consent, in the case of minors both of the person concerned and their parents.
But public prosecutor Isabelle Paganelle warned that "people who say no become potential suspect and detention and searches of premises might be considered".
Although the students were reported to accept the need for the tests, civil rights campaigners are concerned at an erosion of the presumption of innocence.
"This measure is out of proportion, threatening and traumatising," Pierre Tartakowsky of the French human rights league told RFI. "In our system it's up to the legal system to find the guilty party."
Results should be known within a month.