A 31-year-old woman with familial adenomatous polyposis (FAP) was diagnosed with colon cancer. Genetic testing showed a germ cell line mutation of APC (a frame-shift mutation). Moreover, deletion of MSH2/MSH6 protein and high microsatellite instability (MSI-H) was detected. Therefore, Lynch syndrome (LS) associated with FAP was suspected. Additional analysis showed no pathogenic mutation of MSH2 and no change in the number of copies or methylation in the promoter region. Therefore, this was not a case of LS caused by a genetic germ cell line mutation. The chromosome instability had been caused by a malfunction of APC, and it produced a structural change in a gene in the somatic cells. This case is very interesting.