High frequency allelic loss of chromosome 9p21 has been reported in a number of human cancers, including those of the esophagus. The CDKN2 gene on chromosome 9p21 that encodes the p16 inhibitor of cyclinD/Cdk4 complexes is a target of allelic loss and inactivation in a variety of human cancers and cell lines. However, the roles of 9p21 allelic losses and CDKN2 mutations in human neoplastic progression in vivo remain controversial. We determined the prevalence of allelic loss at 9p21 and mutations in CDKN2 in esophageal adenocarcinomas and investigated the order in which they occurred relative to the development of aneuploidy and cancer during neoplastic progression. Aneuploid cell populations from 32 patients with Barrett's esophagus who had premalignant epithelium, cancer, or both, were purified by DNA content flow cytometric cell sorting and evaluated by polymerase chain reaction. Twenty-four of 32 informative patients (75%) had allelic loss at 9p21 in aneuploid cell populations. Premalignant epithelium was available for seven of the patients who had 9p21 allelic losses in cancer; allelic loss of 9p21 was detected before cancer in all seven (100%). Allelic loss of 9p21 preceded the development of aneuploidy in 13 of 15 patients (87%) who had aneuploid cell populations detected in premalignant epithelium, and the two events were detected simultaneously in the remaining two patients. Five of 22 aneuploid populations (23%) with 9p21 loss had somatic mutations in the remaining CDKN2 allele. The same mutations and 9p21 allelic losses were also found in the corresponding diploid cells from premalignant epithelium in all three cases that were evaluable. However, there was no evidence for mutation or homozygous deletion of p16 in the other 17 patients with 9p21 allelic loss. Our results indicate that 9p21 allelic losses and CDKN2 mutations develop as early lesions in diploid cells before aneuploidy and cancer during neoplastic progression in Barrett's esophagus.