We report the molecular characterization of familial adenomatous polyposis (FAP) in the Republic of Macedonia. The incidence (0.25 x 10^–6) and prevalence (2 x 10^–6) of this condition in our country is much lower than described for other European populations. In three out of seven patients analyzed, deletions of various portions of the adenomatous polyposis coli (APC) gene region were detected, which is in agreement with the relatively high frequency of this type of defect in FAP patients. Aberrant APC transcript, inexplainable by a corresponding DNA structural variation, were detected in the peripheral blood lymphocytes of three patients, suggesting that impairment of the normal splicing mechanism may be involved in the pathogenesis of this condition.