We aimed to investigate the distribution of alleles and genotypes of the 3’UTR VNTR polymorphism of SLC6A3 between a sample of patients with bipolar I disorder and healthy controls. We used a cross-sectional, case-control study which was carried out on 100 subjects with bipolar disorder and 50 healthy controls. The bipolar group was divided into three subgroups: 40 with bipolar disorder without psychotic features, 31 with bipolar disorder with mood-congruent psychotic features and 29 with bipolar disorder with mood-incongruent psychotic features. All participants provided a blood specimen for analysis and genomic DNA extraction. The genotypic distribution of DAT 3ˊUTR (SLC6A3) for both patients and controls was within the Hardy–Weinberg equilibrium. For the genotypes of DAT 3 intron VNTR, the gene frequency estimates for the whole sample indicated a significant departure from the Hardy–Weinberg equilibrium. Genotype frequencies showed a significant difference between the bipolar I and the control groups. There was a marginally significant higher frequency of 7/8 3 intron VNTR genotypes in the bipolar I disorder with mood-incongruent psychotic features. Among patients with a positive family history of psychosis in the three bipolar subtypes, the frequency of 3 intron DAT VNTR showed a statistically significant difference in the mood-incongruent group and 7/8 genotype was statistically significant. This study suggests that the 7/8 genotype may predispose a subtype of bipolar disorder characterized by mood-incongruent psychotic features in cases with a positive family history of psychotic disorder.