The loss or inactivation of genes at specific chromosomal loci is one of the important mechanisms during the tumor development in humans. To investigate the role of genetic alterations in the carcinogenesis of gallbladder carcinoma, 32 carcinoma cases and 11 dysplasia cases of gallbladder were analyzed for loss of heterozygosity (LOH) and microsatellite instability (MI) on chromosomal regions 3p, 5q, 8p, 9p, 13q, 17p, and 18q with 17 microsatellite markers. Loss of one allele was identified on chromosomes 5q (55%) and 17p (40%) in dysplasias and on chromosomes 3p (52%), 5q (66%), 9p (52%), and 17p (58%) in carcinomas. LOH on chromosomes 13q and 18q was frequent only in advanced stage (III and IV) carcinomas (40% and 31%, respectively). LOH on chromosome 17p was correlated with intranuclear p53 accumulation. LOH on multiple chromosomes was more frequent in advanced carcinomas with metastasis than in cases without metastasis (P < .05). A widespread MI was observed in only one case of carcinoma. We conclude that LOH on 5q is an early change of carcinogenesis in gallbladder and that LOH on 3p and 9p is related to the progression of gallbladder carcinoma LOH on 13q and 18q is likely to be a late event. LOH on 17p occurs not only in dysplasia but also increases during the subsequent stages. Accumulation of LOH may be associated with carcinogenesis of the gallbladder, but the role of MI may not be significant.