OBJECTIVES: To determine and compare the prevalence of use of anti-diabetic and antilipidemic medications in children and adolescents treated with atypical antipsychotics to those not treated with atypical antipsychotics. METHODS: Virginia Medicaid beneficiaries (between 2 and 17 years) continuously enrolled from August 1, 2010 to July 31, 2011 were included in the study. Subjects with at least two paid prescription claims for aripiprazole, olanzapine, quetiapine, risperidone, or ziprasidone were assigned to the exposed group. All other subjects in the Virginia Medicaid system during the study period were assigned to the non-exposed group. Prevalence of anti-diabetic and antilipidemic medication use in both groups were computed and compared using Chi-square test (α=0.05). Generic Code Numbers were used to identify all medications.  RESULTS: A total of 299,593 patients (2,286,629 claims) were identified as the non-exposed group (mean age: 8.23 +/- 4.70 years, 50.10% males). Of these patients, 0.32% had prescription claims for anti-diabetic medications (mean age: 13.82 +/- 2.67 years, 28.42% males), and 0.087% had prescription claims for antilipidemic medications (mean age: 11.82 +/- 4.93 years, 55.94% males). A total of 5,663 patients had 53,236 claims for atypical antipsychotic agents (mean age:  12.02 +/- 3.63 years, 63.13% males). In this group 1.66% had prescription claims for anti-diabetic medications, and 0.37% had prescription claims for antilipidemic medications. There was a significantly higher rate of anti-diabetic and antilipidemic drug use in the exposed group compared with the non-exposed group (p<0.0001). Among the atypical anti-psychotic users, the highest number of claims was for risperidone (50.98%). The prevalence of antidiabetic medication claims was highest for ziprasidone (7.53%) and the prevalence of antilipidemic medications was highest for olanzapine (1.45%).  CONCLUSIONS: The prevalence of anti-diabetic and antilipidemic medication use was higher among children and adolescents in the Virginia Medicaid population prescribed atypical antipsychotics than those not prescribed atypical antipsychotics.