Genetic factors of alcoholism influence the phenotypic heterogeneity of alcohol dependence, allowing the higher or lower expression of related aggressive behaviours. The pathogenesis of alcoholism and anti-social behaviour has been connected to serotonergic system dysfunction, given support to examine the association with 44-basepair insertion/deletion polymorphism of serotonin gene transporter (5-HTT). The study aims to assess the relationship between 5-HHTLPR polymorphism, aggressive behaviour and alcohol consumption pattern. There were recruited 97 alcohol dependent patients from the alcoholism unit (Etilo-Risco) of the Psychiatric Service of Santa Maria Hospital. Blood for DNA extraction and clinical and behavioural information was collected during the therapeutic program. Regarding 5-HTTLPR polymorphism prevalence in alcoholic population, 30.7% were homozygotic to l allele, 19.8% were homozygotic to s allele and 49.5% were heterozygotic l/s. Alcoholic patients carrying the l allele from 5-HTTLPR genotype showed significant lower scores of aggressivity during acute alcohol consumption, and alcoholic patients carrying the s allele showed significant higher scores of aggressivity (during acute alcohol consumption and abstinence), however, the results were not significant. The association between the functional nature of the s allele of 5-HTTLPR polymorphism with aggressive behaviour is in agreement with the general models of aggressivity that report low levels of central serotonergic activity related to impulsive and anti-social behaviours. The results demonstrate an association between 5-HTTLPR polymorphism and the auto and heteroaggressive behaviour in alcohol dependent population, particularly when aggressivity appears under acute alcohol consumption. During acute alcohol consumption stage, the presence of the l allele may act as a protective factor of aggressive behaviour risk, whereas the results tendency showed the s allele as susceptibility factor. Data suggests that the presence of s allele may confer a genetic vulnerability factor to the development of aggressive behaviour in alcohol dependent subjects, specially, in interaction with acute alcohol consumption stage.