Abstract Handedness in humans and paw preference (PP) in rodents have been associated with neural and physiological correlates, which frequently appear to be sex-specific. The present study examines sex differences in the effects of differential PP on post mortem measures of regional monoamine activity in adult Long-Evans rats. The effects of PP on neuroendocrine function were also assessed by measuring plasma adrenocorticotropic hormone (ACTH) in response to a 30-min restraint stress. Most rats showed strong individual PP. Males (n=27) and females (n=26) did not differ in the direction or strength of their PP with nearly equal numbers of left and right-pawed rats. However, many Sex×PP interactions were noted in regional neurochemical measures, and most effects of PP were bilateral in nature and sex-specific. In males, Left PP (relative to Right PP) was associated with reduced striatal dopamine (DA) levels and amygdala DA metabolism bilaterally. In females, Left PP was associated with a bilateral upregulation of DAergic metabolism in both prefrontal cortex and nucleus accumbens, increased amygdala serotonin metabolism, and a (right) unilateral increase in amygdala DA. As in previous studies, some correlations were also noted between PP and asymmetrical or unilateral monoamine measures. As well, rats with strong PP, independent of direction or sex, had lower basal ACTH and more robust stress responses than rats with weak PP, suggesting a possible adaptive advantage to strong lateralization. Overall, sex differences were found only regarding effects of the direction of PP, not its magnitude. The findings suggest that the direction of PP affects distinct bilateral networks of structures sex-dependently. Such fundamental influences of PP on functional brain organization have implications for a wide array of processes under monoaminergic modulation in these brain regions, and may further our understanding of the numerous human examples of gender and handedness interactions across several modalities.