A patient with atypical phenotypes of Prader-Willi syndrome (PWS) was subjected to investigate genomic copy numbers by microarray-based comparative genomic hybridization analysis. Severe developmental delay, relative macrocephaly, protruding forehead, cardiac anomalies, and hydronephrosis were atypical for PWS. Concurrent deletions of 15q11-13 and 5q35 regions were revealed and identified as paternally derived. The sizes and locations of the two deletions were typical for both deletions. Although each deletion independently contributed to the clinical features, developmental disturbance was very severe, suggesting combined effects. This is the first report of co-occurrence of PWS and STS. The co-occurrence of two syndromes is likely incidental.