Advances in genetics have led to an increased understanding of the role of the genotype on behavioural functioning. The purpose of the present study was to examine differences in intellectual functioning in individuals with Prader-Willi syndrome (PWS) with a paternal 15q11-q13 deletion versus maternal uniparental disomy (UPD) of chromosome 15. Measures of intelligence and academic achievement were administered to 38 individuals with PWS (24 with deletion and 14 with UPD). The subjects with UPD had significantly higher verbal IQ scores than those with deletion (P< 0.01). The magnitude of the difference in verbal IQ was 9.1 points (69.9 versus 60.8 for UPD and deletion PWS subjects, respectively). Only 17% of subjects with the 15q11-q13 deletion had a verbal IQ > or = 70, while 50% of those with UPD had a verbal IQ > or = 70. Performance IQ scores did not differ between the two PWS genetic subtype groups. This is the first report to document the difference between verbal and performance IQ score patterns among subjects with PWS of the deletion versus the UPD subtype.