The serotonin transporter (5-HTT) plays a critical role in regulating serotonergic neurotransmission. There is a substantial literature base that implicates serotonergic neurotransmission in alcohol and drug dependence, and therefore candidate genes for substance abuse include the gene encoding the serotonin transporter protein (encoded by SLC6A4). Two different polymorphisms (Stin2 VNTR and 5-HTTLPR) were examined using PCR method. The hypothesis that SLC6A4 gene polymorphisms may be associated with substance abuse was explored in Russian men with alcoholism (n=99), drug addiction (n=61) and in control group (n=132). Maximum likelihood analysis of haplotype distribution was performed by EH&2LD program. The presence of linkage disequilibrium between the two polymorphisms was demonstrated in men with alcoholism (χ2=16.92,p=0.0002), men with drug addiction (χ2=17.65,p=0.0001) and in controls (χ2=6.61,p=0.037). Our results of haplotype analysis didn't reveal any significant differences in global haplotypes distribution between groups of substance abusers and controls. Further analysis showed overrepresentation of the L10 haplotype among alcoholics compared to controls (χ2=5.62,p=0.018,OR=1.79,95%CI=1.1-2.9). The S12 haplotype had lower frequency in alcoholics compared to that in controls (χ2=4.41,p=0.036,OR=0.66,95%CI=0.43-0.97). Our findings confirm the association of SLC6A4 gene with alcohol dependence, but not with drug abuse in our sample.