• We conducted restriction fragment length polymorphism and methylation pattern analyses on 26 typical and atypical patients with Prader-Willi syndrome who did not have a cytogenetically detectable 15q11-13 deletion and on four patients who did have this deletion and were clinically atypical. Maternal disomy for chromosome 15 was identified in 12 patients and paternal deletions in 15q11-13 were found in three cases. Patients with chromosome 15 abnormalities had typical or near typical presentations, based on published diagnostic criteria. Most of the absent criteria in this group were age-dependent features. The remaining 15 patients, including four previously thought to have a cytogenetically apparent 15q11-13 deletion, had neither chromosome 15 molecular abnormality, and these patients were atypical. Patients with maternal disomy had advanced maternal age, suggesting that nondisjunction is part of the etiology of uniparental disomy. This study suggests that molecular diagnosis is critical in patients with Prader-Willi syndrome who appear clinically atypical or who lack a cytogenetically detectable 15q deletion. Methylation pattern analysis is a useful adjunct diagnostic tool for Prader-Willi syndrome.