Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disease. Patients with FAP develop hundreds to thousands of adenomatous polyps in the colon and rectum during their 2nd or 3rd decades, and one or more of them progress to cancer if left without surgical treatment. The gene responsible for FAP was identified in 1991 and termed the APC (adenomatous polyposis coli) gene. Following identification of APC, a number of germ-line mutations responsible for the development of the disease were found. The purpose of this study was to determine the usefulness of a new method, submerged gel electrophoresis, in the detection of the most-frequent mutation of the APC gene [5-base pair (bp) deletion in codon 1309], especially in the presymptomatic diagnosis of FAP. Genomic DNAs were isolated from peripheral blood of patients and their relatives. We used two methods, electrophoresis on polyacrylamide gel and submerged gel electrophoresis, for the identification of APC gene codon 1309 mutation. After only 110 min PCR fragments of 91 bp and 86 bp (5-bp deletion) were completely resolved on a Spreadex EL300 gel. Our results showed that electrophoresis using Spreadex gels provides a simple and rapid non-radioactive method for determination of the most-frequent germ-line mutations in the APC gene.