Most adult germ cell tumors have a consistent cytogenetic abnormality, i(12p), and are aneuploid. Many pediatric germ cell tumors are biologically distinct from their adult counterparts, particularly endodermal sinus tumors (ESTs) of young children. We report cytogenetic and ploidy analysis of nine ESTs involving children under 3 years of age (four extragonadal and five testicular). Structural abnormalities were present in seven tumors and were identifiable in six: 5/6 had a structural abnormality of chromosome 1, usually terminal deletion of 1p; 5/6 showed 6q deletion; 3/6 had structural abnormalities of 3p; 2/6 showed abnormalities of chromosome 2. None showed an i(12p) or abnormality of chromosome 12. Ploidy analysis of the tumors correlated with the cytogenetic analysis; in particular, the tumor that was cytogenetically normal showed no aneuploid peaks. To determine if a marker chromosome was derived from chromosome 12 or if karyotypically normal cases included nondividing tumor cells, interphase fluorescence in situ hybridization using an alpha satellite probe for chromosome 12 was performed. These studies showed no evidence of an i(12p). We conclude that ESTs in young children show cytogenetic differences from their adult counterparts and that loci on 1p, 6q, and 3q need to be further studied.