The Spontaneously Hypertensive Rat (SHR) model was used to test the hypothesis that a locus on the SHR Y-chromosome is responsible for increased aggression resulting from increased serum testosterone and decreased amygdala serotonin content compared to the WKY Y-chromosome. To examine the Y-chromosome in SHR and WKY males, consomic Y-chromosome strains were used (WKY.SHR-Y and SHR.WKY-Y). Novel resident intruder tests and intra-colony scarring behavioral paradigms were used to measure aggression in a colony environment. Both resident intruder test attack number and wounding, along with intra-colony scarring scores showed the colony males with the SHR Y-chromosome (SHR and WKY.SHR-Y strains) were more aggressive than the colony males with the WKY Y-chromosome (WKY and SHR.WKY-Y strains). The SHR Y-chromosome colony male animals also had significantly higher serum testosterone, as well as overall lower amygdala serotonin content than the WKY Y-chromosome colony male animals. The results suggest that these behavioral and physiological differences between the SHR and WKY strains are a result of a mutation in the non-pseudoautosomal region unique to the Y-chromosome.