BACKGROUND The Prader-Willi syndrome (PWS) is a neurogenetic disorder associated with abnormalities in the chromosomal region 15q11-13 of paternal origin. Most cases (65-85%) have a deletion involving the paternally derived chromosome and the remainder (20-25%) have a maternal uniparental disomy. Some patients have a defect in the imprinting process. We report the results of molecular, cytogenetic and clinical studies on 10 PWS patients. PATIENTS AND METHODS 18 suspected patients were classified as PWS typical or not typical as they fulfilled or not the clinical criteria for PWS. Cytogenic studies-high resolution chromosome banding analyses (HRGTG) and fluorescence in situ hybridization (FISH) -and molecular chromosome genetic analyses--microsatellite markers and Southern blotting--were carried out from peripheral blood lymphocytes. RESULTS PWS was confirmed in 10 probands. 8 fulfilled the clinical criteria for PWS and showed cytogenetic and/or molecular abnormalities. In 2 patients without clinical or cytogenetic data, diagnosis was confirmed by molecular methods only. Cytogenetic and molecular findings describe a characteristic clinical picture of PWS. CONCLUSIONS Cytogenetic techniques (FISH and HRGTG) confirmed PWS diagnosis in 40% of cases, microsatellite studies in 70% of them and Southern blotting (the metilation test) in 100% cases. Southern blotting is the method of choice for rapid diagnostic testing of patients suspected of having PWS.