The incidence of familial adenomatous polyposis (FAP) is approximately 7.4 per 100,000 inhabitants. APC gene mutations have been found in 60-70% of all FAP families, codons 1309 (20%) and 1061 (8%) being known hot-spots. We searched for mutations in the APC gene in a population-based registry of FAP from the Spanish Balearic Islands. Fifty-one members of 12 FAP families registered in the Balearic Islands Cancer Registry were studied; three of them were de novo cases. Mutations in the APC gene were analyzed by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and sequencing. Haplotype was established by combining intra- and extragenic markers. Mutations in the APC gene were detected in 10 out of 12 (83%) families analyzed. Six families shared the same mutation, a 5-bp deletion at codon 1061 (c.3221_3225delACAAA). Five of the families containing this mutation shared the same haplotype and originated in the same geographic area. The codon 1061 mutation in the APC gene is the most common one in the Balearic Islands. Although this codon is a hot-spot, the haplotype analysis of these families is consistent for the presence of a founder effect of the 5-bp deletion at codon 1061 in FAP families in the Spanish Balearic Islands.