Although the biologic significance of germ-cell tumors to the study of malignancy and differentiation has been well recognized for some time, detailed genetic analysis based on fresh tumor biopsies has not been initiated until recently. The first stage of such studies, as with other, more extensively investigated, tumor systems, has been cytogenetic analysis. To date, cytogenetic data on close to 200 tumors are available, which have already yielded valuable insights into the biology of these tumors, as well as a clinically useful marker. Thus, initial correlations between chromosome change and histologic type have been recorded, gene amplification associated with malignant progression has been identified, the cytogenetic basis of malignant differentiation in teratomatous lesions has been clarified, and sites of candidate tumor suppressor genes unique to this system have been identified. The usefulness of i(12p) as a diagnostic marker, especially in tumors of uncertain histologic type, has been established. Because of the clinical usefulness of this marker, molecularly based methods for its detection, without the need for formal cytogenetic analysis, have been developed. Cytogenetic analysis of larger prospectively ascertained series than have been studied so far and analysis of large numbers of tumors utilizing molecular techniques can be expected to yield significant insights into the biology and clinical behavior of these tumors.