BACKGROUND The interaction of environmental and inherited factors determines how a young person becomes involved in problem behaviours such as drinking alcohol. We have investigated whether the association of family relationships with early experience with alcohol is related to variation in the serotonin transporter gene promoter region (5-HTTLPR). METHODS We used data of the two birth cohorts of the Estonian Personality Behaviour and Health Study (original n = 1,238) at age 15 and 18 years. Data were self-reported in a laboratory setting. RESULTS Family relationships at age 15 years were significantly related to the frequency of drinking alcohol. Specifically, association of Warmth in Family (closeness and support within family) with consuming alcohol was in a negative, while maltreatment (misprize and abuse) in a positive relationship with alcohol consumption. At age 18 years, the effects of family relationships on consuming alcohol were lower and no longer statistically significant (p values >0.10). The associations between family relations and alcohol use at age 15 years varied by the 5-HTTLPR genotype: at this age, the impact of the family relations, both Warmth and Maltreatment, on the frequency of drinking alcohol was statistically significant among participants with the S/L genotype, and while rather similar results were obtained for the S/S genotype, no relations were apparent between family relations and consuming alcohol in subjects with the L/L genotype. CONCLUSIONS These findings reveal that family relations are related to alcohol consumption, dependent upon the 5-HTTLPR genotype. This is compatible with the hypothesis that the S-allele carriers are more malleable by the environment.