The tests, a first in a French school, will end on Wednesday and target 475 high school students, 31 teachers and 21 others present on the premises on September 30 when the rape happened.
The schoolgirl was assaulted in the private Catholic Fenelon-Notre-Dame high school in the southwestern Atlantic port city of La Rochelle.
The attack took place after the light from an automatic time switch went off and she therefore could not give the physical details of her attacker.
The cost of the operation will be around 5,000 euros (USD 6,940) and saliva swabs will be taken and matched with DNA found on the girl's clothes.
DNA from her clothes had tested negatively when matched with those of her family and close friends. The results are due out in a month.
Isabelle Pagenelle, the prosecutor of La Rochelle, said both parental and individual authorisation was necessary for minors undertaking the test.
She said there would be no forced DNA testing but added that "those saying no can become potential suspects who may be detained."
The school's principal Chantal Devaux said the rape had hitherto remained a secret and only investigators were in the loop.
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