We aimed to estimate the prevalence and correlates of psychotropic polypharmacy in Brazilian psychiatric patients by gender. Sociodemographic, behavioral and clinical data were obtained through face-to-face interviews and medical charts of 2,475 patients. Psychotropic polypharmacy was defined as the use of two or more psychotropic drugs and occurred in 85.7% of men (95%CI: 83.6%-87.6%) and 84.9% of women (95%CI: 82.8%-86.8%; p > 0.05). The mean number of psychotropic drugs/patient was 2.98 ± 1.23 and most common combinations included antipsychotics. Multivariate analysis showed that for both genders, previous hospitalization, severe mental illness, multiple psychiatric diagnoses and an insufficient number of professionals in the health care unit was associated with psychotropic polypharmacy. However, other correlates such as inpatient care, use of non-psychotropic drugs, living in unstable conditions and current smoking vary among them. Psychotropic polypharmacy was a common practice in this national sample. The results highlighted the need for national guidelines to manage patients with mental illness, considering the difference among genders and disease severity, to reduce the burden of polyphamacy in this population.