Abstract: The serotonin transporter gene polymorphism is associated with plastic reconstructions of the brain structure and activity throughout life, which depend on the sex and age of the subjects. We studied the characteristics of the association between the serotonin transporter gene 5-HTTLPR polymorphism and the background EEG in healthy young (19–35 years, N = 89) and elderly (55–80, N = 60) men. The EEG power, calculated in individual frequency ranges from Δ- to γ-rhythms inclusively, was analyzed. Although the genotyping identified three alleles (SA, LG, and LA), we considered the division into groups with a high (LA/LA), intermediate (LA/LG, LA/SA), and low transcriptional activity (SA/SA, SA/LG), that were marked as L'/L', S '/L ', and S '/S ', respectively. Age-related differences were found in the association of the serotonin transporter gene 5-HTTLPR polymorphism with the power of the background EEG in θ and α1 frequency ranges. Among the L'/L' and S '/L' genotype carriers, elderly men had lower indices of the θ and α1 rhythm powers than young ones. Genetic differences in the power of these rhythms were detected in older men due to lower values in carriers of the S '/L' genotype as compared with S '/S ' and L'/L'. The results obtained contribute to the understanding of the mechanisms of heterogeneity of age-related reconstructions in the brain activity and related changes in mental and affective functions regulated by serotonergic system of the brain.