Human germ cell alkaline phosphatase (GCAP) is developmentally expressed in primordial germ cells and in trace amounts in the testis and thymus. The equivalent mouse isozyme, embryonic alkaline phosphatase (EAP), is similarly expressed in the testis and thymus but also from the 2-cell to blastocyst stage of preimplantation development. EAP has been found to be transiently expressed in M-phase spermatogenic cells in the mouse testis. These alkaline phosphatase isozymes serve as markers of germ cell differentiation and in the management of germ cell tumors. GCAP is expressed in carcinoma-in-situ and seminoma where serum GCAP levels are often elevated and may provide clinically useful information. However, GCAP is a polymorphic enzyme, and monoclonal antibodies to be used in the clinical evaluation of tumor tissues or fluids should be carefully evaluated for their ability to detect all allelic variants of GCAP.