The two tiny female foetuses, between five to seven months in gestational age, were found in King Tut's tomb in Luxor when the tomb was disovered by Howard Carter in 1922.
Zahi Hawass, head of the Supreme Council of Antiquities, said the DNA samples would be compared to each other and to King Tut's mummy. The testing is part of a wider programme to test the DNA of hundreds of mummies to determine their identities and their family relations.
Mr Hawass said the tests could help determine Tutankhamun's family lineage, which has long been a source of mystery.
Scholars believe that at the age of 12, Tutankhamun married Ankhesenamun - a daughter of Akhenaten by his better known wife Nefertiti - but the couple had no surviving children.
There has been no archaeological indication that Tut, who died around the age of 19 under mysterious circumstances over 3,000 years ago, left any offspring.
The council said that if the tiny mummies are unrelated to Tut, they may have been placed in his tomb to allow him to "live as a newborn in the afterlife".
Ashraf Selim, a radiologist and member of the Egyptian team, said the tests could take several months. So far, the team has carried out CT scans on the two fetuses and taken samples for DNA tests.