During the course of screening the 5' half of exon 15 of the APC gene for germline and somatic mutations in two groups of patients, those with the inherited cancer prone syndrome adenomatous polyposis coli (APC) or with sporadic colorectal cancer, we have identified a number of intragenic changes that are not associated with the disease phenotype. Four of these changes are rare variants, each confined to one or two families and not detected in 50 additional unrelated people. Two common polymorphisms, at codon 1493 (exon 15I) and codon 1678 (exon 15J), were extensively investigated and found to be in almost complete linkage disequilibrium not only with each other but with a previously described polymorphism at codon 1960 (exon 15N). The rapid and sensitive single strand conformation assay used provides an efficient method for presymptomatic diagnosis using intragenic variants and was additionally used to show allele loss at the APC locus in sporadic colorectal carcinomas.