To study the possible role of cryptic mosaicism in phenotypical variations of 45,X Turner syndrome, we analyzed low-level mosaicism by methods based on the polymerase chain reaction. For the detection of Y-chromosome-derived fragments, we used three Y-specific primer pairs representing the centromere, Yp11.3, and Yq12. None of the 18 patients with 45,X had Y-derived chromosomes. For the detection of X chromosome mosaicism, we employed a novel modified HUMARA (human androgen receptor) assay, which proved to be a sensitive method with a detection limit as low as 1 in 960 cells. Using this assay, we detected low frequency cryptic X chromosome mosaicism in 2 of 18 cytogenetically 45,X patients.