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A biomarker, according to a generally accepted definition, is a substance or a manifestation used as indicator of a biologic state. It has the characteristic to be objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacological responses to therapeutic interventions. Biomarkers are important tools available to the clinicians with escalating perspectives in oncologic field. Clinical and genetic biomarkers are essential to properly individuate the disease, to address patients to specific surveillance programs and therapeutic strategies. An ideal biomarker should be absent in normal tissue/condition but present in precancerous lesions like dysplasia and so able to recognize early cancer. Coming from these considerations, several of the known genetic pathways in cancer pathogenesis could be considerate potential candidate biomarkers. In this review, we have reported clinical and molecular biomarkers helpful to manage the Familial Adenomatous Polyposis (FAP), a dominantly inherited colorectal cancer predisposition syndrome. Biomarkers, both clinical and molecular, are essential to reduce the high potential morbidity of FAP giving the opportunity to develop innovative diagnostic and therapeutic protocols.