Autistic traits are over-represented in transgender populations, and gender variance is high in autistic individuals. Furthermore, some evidence suggests that the autism/transgender overlap is limited to individuals sex assigned female. Few studies, however, have investigated the impact of this overlap on mental health. This study therefore sought to investigate whether the autism/ transgender overlap confers an increased risk of depression or anxiety. An online study of 727 individuals revealed a substantial overlap between transgender identity and autism, with increased autistic traits found in trans men compared to trans women. Depression and anxiety were highest in autistic-trans individuals, but no superadditive effect was observed. The implications of these findings are discussed in relation to the wider healthcare system.