We have evaluated possible contributions of HLA-DRB1 alleles to autism spectrum disorder (ASD) in 103 families of Caucasian descent. The DR4 allele occurred more often in probands than controls (0.007), whereas the DR13,14 alleles occurred less often in probands than controls (p = 0.003). The transmission disequilibrium test (TDT) indicated that the ASD probands inherited the DR4 allele more frequently than expected (p = 0.026) from the fathers. The TDT also revealed that fewer DR13 alleles than expected were inherited from the mother by ASD probands (p = 0.006). We conclude that the TDT results suggest that DR4 and DR13 are linked to ASD. Reasons for the parental inheritance of specific alleles are poorly understood but coincide with current genetic research noting possible parent-of-origin effects in autism.