The aim of this study was to determine the location of antipsychotic-induced weight gain in drug naïve, first episode patients with schizophrenia. Various fatness and fat distribution parameters (by Computerized Tomography scanning and anthropometry) and 1600 hr plasma cortisol were measured in 19 (15 men and 4 women) subjects with schizophrenia (mean age = 31.0 years; mean body mass index [BMI] = 24.6 kg/m2) and an equal number of age- and sex- matched controls (mean age = 32.6 yr; mean BMI = 23.0 kg/m2). Patients were then given either olanzapine or risperidone. Sixteen patients were re-tested following a treatment period lasting approximately 6 months. Patients with schizophrenia, had significantly more intra-abdominal fat [IAF] (116.8 +/- 20.2 cm2 vs. 38.0 +/- 4.8 cm2, respectively; t = 3.80, df = 18, p < 0.0001) and had higher levels of plasma cortisol (360.2 +/- 49.6 nmol/L vs. 192.7 +/- 19.7 nmol/L, respectively; t = 3.13, df = 18, p < 0.003) than appropriately matched control subjects. Treatment with atypical antipsychotics did not result in a significant increase in IAF (116.8 +/- 20.2 cm2 vs. 131.7 +/- 20.9 cm2; p = NS) though visceral fat stores still remained significantly higher than those seen in controls (38.0 +/- 4.8 cm2) (F = 9.34; df = 2, 51; p < 0.0003). However, plasma levels of cortisol did significantly decrease (360.2 +/- 49.6 nmol/L +/- vs. 316.2 +/- 48.4 nmol/L; p < 0.05). Pre-treatment levels of IAF did not differ between those who received risperidone and those who were given olanzapine (123.0 +/- 35.9 cm2 vs. 113.1 +/- 15.7 cm2, respectively; t = 0.20, df = 16, p < 0.84). The increase in IAF did not differ between those given risperidone and those who received olanzapine (26.9 +/- 12.1 cm2 vs. 18.24 +/- 11.44 cm2, respectively; t = 0.50, df = 16, p < 0.63). Patients with drug naïve, first episode, schizophrenia have higher levels of visceral fats stores as compared to matched control subjects. Treatment with atypical antipsychotics does not result in a significant increase in IAF distribution.