Over the last two decades, prescriptions of second-generation antipsychotics (SGAs) to children have increased significantly. During this time period, there has also been a growing body of literature demonstrating an increased risk of metabolic complications in children treated with SGAs. Prospective studies clearly suggest that SGAs confer increased risk for development of weight gain and dyslipidemia over the short term (<3 months). Although long-term SGA use in children is a common practice, investigation of metabolic complications over the long-term is limited to retrospective reports. Thus, we conducted a prospective longitudinal study to assess the impact of SGAs on metabolic complications during the first 12 months of treatment. To determine the risk of developing obesity and related metabolic complications in children following long-term treatment with risperidone or quetiapine. This was a one-year naturalistic longitudinal study conducted between February 2009 and March 2012. A total of 115 children aged two to 18 years without prior exposure to SGAs were enrolled at initiation of treatment with either risperidone or quetiapine. Metabolic parameters were measured at baseline and months 6, and 12. Data of 37 participants (20 risperidone-treated and 17 quetiapine-treated) who completed 12 month monitoring were used in the analysis. After one year of SGA treatment, mean weight increased significantly by 10.8 kg (95% CI 6.6, 10.5 kg) for risperidone and 9.7 kg (95% CI 6.5, 12.8 kg) for quetiapine. BMI z-score also increased significantly in both groups (P<0.001). There was a high incidence of children becoming overweight or obese [6/15 (40.0%) for risperidone-treated and 7/14 (50.0%) for quetiapine-treated]. The mean levels of fasting glucose (for risperidone-treated) and ratio of total cholesterol to HDL cholesterol (for quetiapine-treated) increased significantly by 0.23 mmol/L (95% CI 0.03, 0.42 mmol/L) and 0.48 mmol/L (95% CI 0.15, 0.80 mmol/L), respectively. Children treated with risperidone or quetiapine are at a significant risk for developing obesity, elevated waist circumference and dyslipidemia over 12 months of treatment. These data emphasize the importance of regular monitoring for early identification and treatment of metabolic side-effects.