Twenty three patients with a putative diagnosis of Prader Willi syndrome (PWS) were reassessed clinically and then examined by cytogenetic and molecular techniques. Nineteen patients fulfilled the diagnostic criteria for PWS and the remaining four were judged to have atypical PWS. Definite molecular defects were detected in all clinically typical PWS patients but one. A deletion of part of chromosome 15q could be identified molecularly in 14 patients (74%) and maternal disomy for chromosome 15 in four (21%). In all, except one, PWS patients with molecularly detected deletions, the deletion was also identified by cytogenetic studies. Cytogenetic deletions were suspected in two of the atypical PWS patients. However, based on the results of scoring the diagnostic criteria for PWS and on the PW71B methylation test, we were able to rule out PWS in all of our atypical patients. Our study confirms observations that both clinical and cytogenetic investigations can provide misdiagnoses of PWS in some patients, and the first, simple and fast investigation, which can confirm the PWS in most, if not all PWS patients, is molecular analysis by the methylation test.