Background: Pharmacological, neurobehavioral, and therapeutic evidence have implicated serotonin in the pathogenesis of depression. There are conflicting reports on the association of genetic variants of serotonin transporter gene (5-HTTLPR) with major depressive disorder. The 5-HTTLPR is thought to have three primary allelic variants (rs25531): LA, LG, and S. The present study examined whether major depression was associated with tri-allelic 5-HTTLPR polymorphisms in a Han Chinese population. Materials and Methods: Bi-allelic and tri-allelic 5-HTTLPR polymorphisms were assessed in 305 patients with major depressive disorder (MD) and 313 unrelated healthy control subjects. In addition, to reduce clinical heterogeneity, subtype analyses were performed for clinically important variables, including family history of major affective disorder, age at onset, and severity of MD. Results: The bi-allelic 5-HTTLPR polymorphism was not associated with MD and its clinical subgroups. However, the tri-allelic 5-HTTLPR polymorphism was associated with major depression and with specific subgroups. In particular, in male subjects, patients with a low expressing genotype (S’/S’) were at higher risk for MD than those with high expressing genotypes (S’/L’ and L’/L’). This positive association was only observed in the subgroups of late-onset and moderate severity MD. Conclusions: The present study suggests that the tri-allelic 5-HTTLPR polymorphism might be a risk factor for susceptibility to either MD or its clinical subtypes in the Han Chinese male population but not in the female population. However, these results should be validated in a larger patient population that includes different ethnic samples or subdiagnosis groups.