Size and colour are frequently subject to sex-specific sexual selection, with males often larger and more colourful than females. But can this selection also influence brain development? The role of sexual selection in altering brain organisation and structure over evolutionary time is still poorly understood. We use a group of lizards, the genus Ctenophorus, that are ideal for examining the role of sexual selection in shaping the evolution of the brain. Ctenophorus lizards vary in their level of sexual dimorphism from monomorphic, inconspicuous species to highly ornamented (colourful) males. The Ctenophorus phylogeny shows that sexual dimorphism has evolved multiple times across different clades with the genus. In this study we have selected multiple sexually dimorphic and monomorphic species from across the phylogeny for a comparative analysis of brain structure. We use sexual dimorphism as a proxy for the intensity of sexual selection and ask: do dimorphic species invest more heavily in brain regions associated with reproduction and sexual behaviours? To examine this question, we use both magnetic resonance imaging and fluorescent Nissl staining. We found that males from sexually dimorphic species have a larger pre-optic area of the hypothalamus, which is associated with male sexual behavior. In contrast, males from monomorphic species have larger ventro-medial hypothalami, a region that is associated with female sexual behavior and feeding motivation. In the habenula, a control brain region, there was no difference between sexually dimorphic and monomorphic males. Our results suggest that like colouration, size, shape, and behavior, sex-specific selection pressures can indeed influence brain development.