Trophoblastic tumors represent a unique group of human neoplasms because they are derived from fetal tissue. Except for choriocarcinoma, the neoplasms that develop from human trophoblast are poorly characterized. Placental site trophoblastic tumors and epithelioid trophoblastic tumors are thought to arise from intermediate (extravillous) trophoblasts based on histopathological studies, but direct molecular evidence of a trophoblastic origin has not been established. In this study, we performed molecular analysis in an attempt to confirm their presumable trophoblastic origin. We demonstrated that such tumors contain a Y-chromosomal locus and/or new (paternal) alleles not present in adjacent normal uterine tissue in all 31 informative cases. Loss of heterozygosity was found in 60% of tumors and all 42 tumors assessed contained wild-type K-ras. All of the trophoblastic tumors were heterozygous in at least 1 of 10 single-nucleotide polymorphism markers studied in contrast to homozygosity in all 10 single-nucleotide polymorphism markers in most complete hydatidiform moles indicating that these tumors are not related to complete hydatidiform moles. This study provides the first molecular evidence that placental site trophoblastic tumors and epithelioid trophoblastic tumors are of fetal (trophoblastic) origin.