The serotonin transporter (SERT) gene is a particularly interesting candidate for genetic involvement in affective disorders owing to its role in both the regulation of serotonergic neurotransmission and the mechanism of action of many antidepressant drugs. In this study, variability in the SERT gene was analyzed for the first time in a sample of patients with major depression with melancholia (MDDM) in the context of a genetic association study. Two different polymorphisms of the SERT gene (17q11.1-17q12) were analyzed: a variable number of tandem repeats (VNTR) polymorphism in intron 2, and a deletion/insertion polymorphism (5-HTTLPR) in the promoter region of the gene, the short variant of which (allele 484) reduces the transcriptional efficiency of the SERT gene. Our sample consisted of 74 unrelated subjects who strictly met DSM-IV criteria for MDDM and 84 healthy controls, all of Spanish origin. The analysis of haplotype distribution for both polymorphisms showed significant differences between cases and controls (log-likelihood ratio chi2=11.15, df=4, P=0.025). Moreover, when the frequencies of the 484-STin2.10 haplotype were considered in comparison with any other haplotype combination, a significant increase in this haplotype was found in patients with MDDM [z=2.53 (95% CI, 1.21-5.34), P=0.007]. According to these results, variability in the SERT gene has a small effect on liability to MDDM. Our findings are compatible with an additive effect of both the 484 low-activity allele and a mutation elsewhere within the transporter gene or a susceptibility locus nearby in linkage disequilibrium with the VNTR marker.