To define the relative frequencies of genetic instability in stromal and epithelial compartments during ulcerative colitis (UC)-associated tumorigenesis, samples from laser-captured microdissection were assessed for microsatellite instability and loss of heterozygosity in regenerative tissue, dysplasia, and carcinomas in long-standing UC cases. Five National Cancer Institute-recommended standard markers and four markers located close to p53 and BRCA1 genes in chromosome 17 were tested, and p53 gene sequencing was also carried out. Although chromosome 17-MSI and -loss of heterozygosity in epithelium correlated with histological progression, in stroma they showed a consistently high frequency throughout the different stages, indicating a distinct carcinogenesis pathway of UC. The rates for standard markers were lower in both epithelium and stroma.