To explore the involvement of serotonin transporter (5HTT) in mood disorder, we studied two polymorphisms of the 5HTT gene (a variable number of tandem repeats in the second intron (VNTR) and a 44 bp insertion/deletion in the 5HTT linked polymorphic region (5-HTTLPR)) in a sample of unipolar and bipolar patients and controls. Homozygosity for the short variant of the 5-HTTLPR was significantly more frequent in bipolar patients than in controls (chi2 = 4.68, d.f. = 1, P = 0.03) whereas there was no difference between bipolar patients and controls for allele distribution, suggesting a recessive effect. The interaction between the two markers suggests that the two polymorphisms probably have independent effects to determine the susceptibility to affective disorder. Further studies are required to identify the precise phenotype associated with 5HTT polymorphisms in depressed patients.