We analyzed claims data from the Taiwan National Health Insurance database, which contains data of 23.5 million Taiwan residents. We included children born after January 1, 2000 who had received a diagnosis of autism spectrum disorders (ASD). Patients who were not diagnosed with ASD were included in the control group. The ASD prevalence was 517 in 62,051 (0.83%) children. Neonatal jaundice, hypoglycemia, intrauterine growth retardation (IUGR), and craniofacial anomalies (CFA) differed significantly between the ASD and control groups. After logistic regressive analysis, the adjusted odds ratios of IUGR, CFA, neonatal hypoglycemia, and neonatal jaundice were 8.58, 7.37, 3.83, and 1.32, respectively. Those insidiously perinatal risk factors, namely CFA, IUGR, neonatal hypoglycemia, and neonatal jaundice, could increase the risk of ASD.