We performed flow cytometry and cytogenetic analysis of 37 adenocarcinomas of the distal esophagus and cardia, of which 22 arose in Barrett's mucosa. Two of eight analyzed specimens of Barrett's mucosa had clonal chromosomal abnormalities. In 19 cases clonal chromosomal abnormalities were found in tumor tissue. The complex pattern of cytogenetic changes did not differ among the adenocarcinomas arisen in Barrett's esophagus, and those in the distal esophagus without Barrett's mucosa or cardia. Abnormal karyotypes with multiple and complex rearrangements were seen in 11 cases and with single or a few numeric changes in eight. Losses of chromosomes 4, 18, 21, and Y were the most frequent numeric changes. Loss of the Y chromosome was observed in eight of 26 tumors of males (31%). Gains of chromosomes 14 and 20 were also frequent numeric changes. Structural abnormalities were observed in 13 of the abnormal karyotypes (68%). The chromosome arms most frequently rearranged were 1p, 3q, 11p and 22p. The chromosome arm most frequently contributing to losses was 1p, with the shortest region of overlap being 1p22-33. The chromosome arms most often involved in gains were 11p and 22p, and i(3q) was the isochromosome that was most frequently identified.