Abstract: Specific genotypes of the rhesus monkey and human serotonin transporter gene (SERT) promoter region are associated with personality traits and serotonergic activity. However, the most commonly studied promoter polymorphism (5-HTTLPR) is monomorphic in many other monkey species. To date, no systematic search for alternative potentially functional polymorphisms across the remaining coding parts of the gene has been undertaken in other primate species, despite the crucial role SERT plays in modulating serotonergic tone. We investigated whether sequence variation in this gene is associated with social rank and serotonin metabolite (5-HIAA) differences in 524 cynomolgus macaques. Sequence variation and extent of linkage disequilibrium (LD) across the regulatory and coding regions were initially characterized in 92 macaques. The exons and promoter contained 28 polymorphisms, more than double that recorded for human SERT. In further contrast to humans, the macaque SERT showed no significant LD. Potentially functional polymorphisms were genotyped in all animals. No individual variants or haplotypes were significantly associated with social rank or 5-HIAA concentrations; however, certain serotonin transporter diplotypes may modulate acquisition of dominance status.