Merkel cell carcinoma or small cell carcinoma of the skin is a rare skin cancer seen in increasing numbers in Queensland, Australia. In its clinical course and histopathology, it resembles small cell lung carcinoma (SCLC). Little is known of the genetic basis of this disease except for a number of cytogenetic studies and three loss of heterozygosity studies. Therefore, comparative genomic hybridization was performed to determine the characteristic DNA gains and losses that occur in this tumor. Comparative genomic hybridization analysis of 34 specimens from 24 patients revealed a pattern of gains and losses that closely resembles that seen in SCLC. Overall frequent loss was seen for chromosomes 3p (46%), 5q (21%), 8p (21%), 10 (33%), 11q (17%), 13q (33%), and 17p (25%). Significant gains were seen for chromosomes 1 (63%), 3q (33%), 5p (38%), 8q (38%), 19 (63%), and X (41%), with smaller numbers having gains for chromosomes 6, 7, 20, and 21. In contrast to SCLC, amplification in Merkel cell carcinoma is a rare event.