OBJECTIVES: To compare patterns of psychotropic medication use and the associated costs among children with autism spectrum disorder (ASD) between public and private insurance to bridge a knowledge gap in the literature. METHODS: Retrospective analyses were done using year 2003 claims data from Medicaid and the MarketScan databases, a national sample of privately insured individuals. Two-sample z-tests were used to compare the proportions. T-tests were used to compare the means given the large sample size. RESULTS: A total of 18,166 children with ASD were identified in Medicaid and 2,716 in MarketScan. Psychotropic medication was used by 86% of ASD children in Medicaid and 78% in MarketScan. The psychotropic medication costs per ASD patient were nearly twice higher in Medicaid ($1464 vs. $796, p<0.0001). The twelve most costly psychotropic drugs accounted for 82% of all psychotropic drug costs, with Medicaid spending more on all these drugs. Risperidone, the most costly drug in both systems, cost $391 per ASD patient in Medicaid and $218 in MarketScan. The higher Medicaid cost was due to more users (27% vs. 18%) and higher average cost per risperidone user ($1612 vs. $1242). Though the unit cost was similar, the average length of therapy was longer in Medicaid (241 vs. 210 days). Similar patterns existed for other drugs such as olanzapine, the second most costly psychotropic medication in Medicaid. Medicaid had more olanzapine users (7.4% vs. 4.5%), higher costs per olanzapine user ($2276 vs. $1302) due to more days supplied (211 vs. 156 days), with the unit cost being similar. CONCLUSIONS: Children with ASD in Medicaid had much higher psychotropic drug costs than those in commercial insurance. Similar drugs were used, but the same drugs cost much more in Medicaid, due to a higher percentage of children on the medication and a greater duration of use.