Most patients with Prader-Willi syndrome have a deletion of 15q11-13 or maternal uniparental disomy for chromosome 15. The shortest region of deletion overlap is presently defined by the gene for the small nuclear ribonucleoprotein N (SNRPN). We have investigated the integrity of SNRPN as well as the methylation status of D15S63 (PW71) in two patients with apparently normal chromosomes 15 of biparental origin. SNRPN is normal in one patient and deleted in the other one. Both patients are intact at the D15S63 locus, but have an abnormal methylation pattern. These results suggest that a DNA sequence close to SNRPN determines the methylation status of D15S63 and that the methylation test does not only detect the common deletions and uniparental disomy, but other rare lesions as well.