Prader Willi syndrome (PWS) is a developmental disorder caused by a deficiency of paternal contribution of the chromosome region 15q11.2 q13 arising from differently sized deletions, maternal disomy, or rarely imprinting mutations. We have analyzed 20 PWS patients using combined cytogenetic high resolution technique (HRT), fluorescence in situ hybridization (FISH) and molecular studies to identify parental origin (uniparental disomy) or molecular defect (deletion) of the Prader Willi region. Lack of a paternal copy of 15q11.2 q13 resulting from its deletion was found in 16 patients. Using high resolution GTG banding on prometaphase chromosomes, deletion in the 15q11.2 q13 region was detected in only 8 patients. Application of FISH with different sets of PWS specific unique sequence probes (D15S11, SNRPN, D15S10, GABRb3) revealed microdeletions in 12 patients. In 12 out of 20 cases FISH confirmed HRT studies, while in 8 cases inconsistent results were obtained. No discrepancies between results of FISH and molecular studies were found, although the latter had a higher sensitivity. We conclude that FISH appears to be a rapid and reliable method of microdeletion identification and should be performed as a method of choice in cytogenetic diagnosis of Prader Willi syndrome.