Gender variance is a broad term used to describe gender non-conforming behaviors. Past studies have used the parental response to Child Behavior Checklist (CBCL) Item 110, which asks whether a child “Wishes to be of opposite sex” as an indicator of gender variance. The population prevalence of gender variance in children and adolescents using this metric was found to be 1.2% in birth-assigned females and 0.4% in birth-assigned males (Achenbach & Rescorla, 2001). However, in those referred for psychiatric evaluation, it was higher (5.4% of birth-assigned females and 2.8% of birth-assigned males) (Achenbach & Rescorla, 2001). The aim of this study was to use the CBCL to estimate the prevalence of gender variance among children and adolescents with neurodevelopmental and psychiatric conditions and assess whether this was higher compared to controls. The response to the CBCL and the child’s neurodevelopmental and/or psychiatric diagnosis were extracted from the clinical notes of 1553 children and adolescents referred to an outpatient psychiatry clinic in Australia. This was compared to data from 181 control participants as well as to the CBCL standardization sample of 1605 controls. Of the 1553 young people, whose mean age was 10.9 years, gender variance was reported in 3.1% compared to 1.7% in local control participants (p > .05) and 0.7% in the CBCL controls (p < .0001). Rates varied depending upon the underlying diagnosis (ASD 5.2%; ADHD 2.5%, intellectual disability 4.7%; depression 2.6%; and anxiety 4.7%). In this way, our findings support past observations that young people with neurodevelopmental and psychiatric conditions have high rates of gender variance.