<i>Background:</i> Monoamine oxidase B (MAO-B) enzyme is involved in the oxidative metabolism of dopamine. We studied whether the A644G polymorphism in intron 13 of the <i>MAO-B</i> gene is a risk factor for schizophrenia. <i>Methods:</i> 242 subjects diagnosed with schizophrenia and related disorders and 290 hospital-based controls participated in the study. Genomic DNA was isolated from whole blood and genotyped with the allele-specific oligonucleotide polymerase chain reaction method. <i>Results:</i> This polymorphism was studied by diagnosis subgroups and the G allele was identified as a risk factor for developing schizophrenia (p = 0.006). When we performed a sex-specific analysis, the G allele was only a risk factor for developing schizophrenia in women (p = 0.01). Although the frequency of the G allele is higher in male patients than in male controls, no statistically significant association with schizophrenia was found. <i>Conclusion:</i> Our results support the involvement of the <i>MAO-B</i> gene in schizophrenia, particularly in women.