Two well known polymorphic regions of the serotonin transporter gene (SLC6A4) are the 5HT-TLPR which consists of a 44-bp insertion or deletion in the promoter region and the STin2 consisting of variable number of tandem repeats in the second intron. Several studies focused on the association of the 5HTTLPR and behavioral or clinical factors of depression; on the other hand, the relation of the STin2 to major depressive disorder (MDD) is less widely investigated. We carried out a case-control study of 71 MDD patients and 99 healthy control subjects comparing frequencies of the STin2 allele- and genotype variants in the two populations. We found a significantly higher frequency of the STin2 10/10 homozygous genotype in the MDD patients' group compared to controls (chi2 = 6,01, df = 2, p < 0.05). To further explore possible endophenotypes of neurocognitive functioning in the background of this disorder we measured performance of 71 cases and 30 matched controls using several tests of neurocognitive functioning. Our results indicated cognitive dysfunctions of the MDD patients in all tests as compared to control individuals. The clinical subgroup with at least one copy of the 10-repeat allele showed a decreased interference threshold in Stroop III as compared to patients without the 10-repeat allele. Average performance of the clinical subgroup without the 12-repat allele proved to be significantly weaker in the working memory and recall tasks (RAVLT) compared to patients having at least one copy of the 12-repeat allele. After further confirmation our results suggest that the presence of STin2.10 and absence of STin2.12 allele may be defined as a possible genetic endophenotype for cognitive dysfunctions detected in MDD.