Cytogenetic investigation of untreated uveal melanoma has shown that the most frequent abnormality is monosomy 3, which occurs in approximately 60% of cases. One of our cases showed distinct pigmented and nonpigmented areas at gross dissection; representative tissue was collected separately from each area, cultured, and harvested using standard cytogenetic techniques. On histologic examination, the pigmented area was found to be composed of small epithelioid cells, whereas the nonpigmented area contained large, pleomorphic epithelioid cells. The karyotype of the pigmented tumor revealed monosomy 3, whereas the nonpigmented tumor showed two apparently normal chromosomes 3. Our purpose in the present study was to investigate the two tumor areas by molecular techniques to determine whether the karyotype of the nonpigmented tumor evolved directly from the pigmented tumor with duplication of the remaining chromosome 3 or whether the two sublines evolved in a divergent fashion from a common precursor stemline. DNA was extracted from normal lymphocytes and separately from both areas of the tumor. The DNA was analyzed using the polymerase chain reaction for polymorphic dinucleotide and tetranucleotide repeat sequences on chromosome 3. Both pigmented and nonpigmented areas of the tumor showed loss of heterozygosity at all informative loci on chromosome 3 that were tested. These results support our hypothesis that an abnormality on chromosome 3 plays a central role in the molecular pathogenesis of uveal melanoma and that some melanomas develop acquired homozygosity (isodisomy) by loss and duplication of the remaining, presumably abnormal, chromosome 3.