Efficacy differences among antipsychotics are relatively small and difficult to predict, however, differences are generally larger and more predictable regarding adverse effects. Antipsychotic related metabolic and endocrine abnormalities are most worrisome, as they are risk factors for cardiovascular morbidity and mortality. Importantly, children and adolescents may be more sensitive to antipsychotic related adverse events than adults, including developmentally inappropriate weight gain and glucose, lipid and prolactin abnormalities, which can be associated with adverse physical outcomes during childhood. Careful selection of an antipsychotic, as well as proactive monitoring and management of side effects should be part of routine clinical practice. Because children and adolescents undergo expected physical changes, it is important to use developmentally appropriate thresholds for weight and metabolic measures. Research is required to elucidate risk factors, mechanisms and best interventions for antipsychotic related adverse endocrine and metabolic effects in pediatric patients.