We studied the association between specific congenital syndromes and autism spectrum disorders (ASD) in the large Finnish Register material. Our data include all children diagnosed with ASD (n = 4441) according to Finnish Hospital Discharge Register in 1987-2000. Four controls per each case were matched to sex, birthplace, date of birth (±30 days) and residence in Finland (n = 17,695). The prevalence of specific congenital syndromes in the Finnish Register of Congenital Malformations was evaluated among the ASD group and the controls by sex. The results of this study suggest that there is an association between several etiologically different syndromes and ASD when compared to controls without ASD. Statistically significant associations were observed with 47,XYY, Sotos syndrome, neurofibromatosis I, and syndrome not otherwise specified. Syndromes were more common among males with ASD compared to controls. These results support the previous studies of etiological heterogeneity of ASD and have importance in clinical examination, management and rehabilitation.