Amniocentesis is, unlike the previously described screening tests, an invasive diagnostic method. A sample is taken with a needle from the amniotic fluid and cell culture is analyzed to determine the presence of numerical and structural chromosomal aberrations. In case of twin pregnancy, amniocentesis has to be performed twice, in order to check both babies.

The results are available in approximately two weeks if a cytogenetic analysis is performed or 2 to 3 days in the case of the QF-PCR method (Down syndrome, the most common disorder), Edwards syndrome, Patau syndrome and Turner syndrome).