For gender determination of preimplantation embryos or circulating fetal cells in maternal blood, we developed a multiplex polymerase chain reaction assay from a single cell. This assay which co-amplifies X (DXZ1)- and Y (DYZ1)-specific repeat sequences, yields a 308-bp band in females and two bands of 154 and 308 bp in males. In a randomized, blinded assay of 100 isolated single amniocytes, 99 (99%) were amplified successfully. All 50 of the XY cells were correctly diagnosed as male (100%), whereas 49 of the 50 XX cells were diagnosed as female (98%). This accurate and efficient assay may be applicable in these clinical settings.