Schizophrenia is a severe brain disorder with an excess morbidity and mortality partly due to a higher incidence of metabolic disturbances and cardio-vascular events. The exposure to antipsychotic treatment has been observed linked to these metabolic abnormalities. This study explores the metabolic effects of aripiprazol, quetiapine and ziprasidone in drug-naïve patients with a first-episode of psychosis, at long-term. Two-hundred and two patients with first-episode of psychosis were included in the study. Patients were randomly assigned to receive quetiapine, ziprasidone, or aripiprazole. Clinical, sociodemographic and anthropometric measures, as well as lipid and glyceamic parameters, were recorded at baseline and after three years of initiating antipsychotic treatment. Body weight and BMI increased significantly after 3 years of follow-up (F = 35.0, p<0.001; and F = 37.6, p<0.001, respectively). Most of the increase in weight occurred within the first year of treatment. The proportion of patients meeting criteria for obesity (5.6% vs 25.7%; p<0.001), hypercholesterolemia (23.2% vs 41.7%; p<0.001) and hypertriglyceridemia (5.8% vs 23.0%; p<0.001) increased significantly. Head-to-head comparisons between antipsychotic groups revealed that the ziprasidone group presented significantly smaller increments in weight (p = 0.034) and BMI (p = 0.020) than aripiprazole group. After 3 years of having presented a first episode of psychosis, patients show significant increments in body weight and BMI, as well as in lipid and glycaemic parameters leading to clinical metabolic disturbances. In this context, the first year is the critical period for weight gain and development of metabolic changes. In this study, ziprasidone produced smaller weight gain than aripiprazole.