Family, twin, and adoption studies show that psychiatric diseases including bipolar disorder (BP) and unipolar disorder (UP) have a substantial genetic component. For these illnesses, both positive and negative associations have been reported for two polymorphisms located in the serotonin transporter gene (5‐HTT) on chromosome 17: a 17‐base‐pair (bp) variable‐number tandem‐repeat (VNTR) in intron 2 and a 44‐bp insertion/deletion in the promoter region. Thus, associations between these 5‐HTT polymorphisms and affective disorders remain unclear. The present work investigates these potential associations in meta‐analyzes that maximize the power to find associations between each disease and the two 5‐HTT polymorphisms. We applied meta‐analysis techniques to case‐control studies of two 5‐HTT polymorphisms and two affective disorders (BP and UP), resulting in four meta‐analyzes. For each polymorphism, we assessed the evidence for allelic associations, heterogeneity among studies, the influence of individual studies, and the potential for publication bias. The short allele(s) of the 44‐bp insertion/deletion polymorphism showed a significant association for BP (odds ratio (OR) = 1.13, P = 0.001) but not UP. For the 17‐bp VNTR, an increase in the number of tandem repeats had no significant association with any of the disorders. The small but significant effects of the 44‐bp insertion/deletion polymorphism for BP is consistent with being one of many genes that contributes to the multi‐factorial nature of these psychiatric disorders. © 2004 Wiley‐Liss, Inc.