The aim of this study was to evaluate the association between autism spectrum disorders (ASD) with and without intellectual disability (ID) and congenital anomalies (CAs) by organ system. The sample included all children diagnosed with ASD (n = 4441) from the Finnish Hospital Discharge Register during 1987-2000 and a total of four controls per case (n = 17,695). CAs of the eye, central nervous system, and specific craniofacial anomalies were most strongly associated with ASD. Children with ASD and co-occurring ID were more likely to have CAs compared to ASD children without ID. The results suggest that some cases of ASD may originate during organogenesis, in the early first trimester of pregnancy. The results of this study may be useful for identifying prenatal etiological factors and elucidating the molecular pathogenesis of ASD.