We previously have demonstrated by comparative genomic hybridization that 80% of ulcerative colitis-related cancers show loss of all or part of chromosome 18, the site of at least three candidate tumor suppressor genes: DCC, SMAD2, and SMAD4. To determine whether these genes are targeted in colitis-related carcinogenesis, we performed a high-resolution analysis of chromosome 18 alteractions in 32 colitis-related colorectal cancers by assessing allelic imbalance at 11 microsatellite markers distributed along the chromosome, and by the quantitative polymerase chain reaction (PCR) method (TaqMan). TaqMan analysis was used to determine the relative copy number of five test genes on chromosome 18 (PACAP on 18p and DCC, SMAD2, SMAD4, and GALNR on 18q). We found allelic imbalance, as assessed by loss of heterozygosity, in at least one marker on chromosome 18 in 25 of the 29 tumors (86%) successfully tested. In 14 tumors, allelic imbalance was detected at all informative markers on 18q, while the other 11 tumors showed only partial loss. Allelic imbalance was most commonly detected at D18S363 (78% of informative cases). This marker is in closest proximity to SMAD4. By quantitative PCR analysis, a relative loss of copy number of SMAD2, SMAD4, and DCC were detected in 40%, 57%, and 53%, respectively, of the colitis-related cancers. SMAD2 was retained in four tumors having loss of SMAD4 and DCC. Loss of SMAD4 alone was seen in one tumor. The present data indicate that the loss of SMAD4 and DCC occurs in the majority of colitis-related cancers.