In the present study, genetic variation of the 5-HT5A receptor was analyzed in patients affected by affective disorders and healthy controls. The sample consisted of 181 patients with major depression, 88 patients with bipolar affective disorder (BP) and 157 unrelated controls (C), all of Spanish origin. Two polymorphisms (-19G/C and 12A/T) in the 5-HT5A receptor gene were analyzed by polymerase chain reaction amplification and subsequent enzyme digestion. No genotype, allele or haplotype differences were found when we compared patients and controls. When clinical variables were considered as possible tools for detecting genetic heterogeneity, no differences were found. Our results suggest that the polymorphisms analyzed in the 5-HT5A receptor gene do not play a major role in the pathogenesis of affective disorders.