The Indigenous populations of Australia and New Zealand are considered at higher risk of mood and anxiety disorders but many studies do not include direct comparisons with similar non-Indigenous controls. We conducted a systematic search of relevant electronic databases, as well as snowballing and targeted searches of the grey literature. Studies were included for meta-analysis if they compared rates of mood and anxiety disorders between Indigenous and non-Indigenous Australians or Maori. Seven Australian and 10 NZ studies were included. Overall, Indigenous people in both countries did not have significantly higher rates of disorder. However, in terms of specific disorders, there were differences in risk by gender, country (Australia or NZ), disorder type, and prevalence (current, 12-month or lifetime). For instance, Indigenous Australians and Maori both had significantly lower rates of simple phobias (current prevalence) and Maori participants had significantly lower rates of both lifetime simple phobia and generalised anxiety disorders. By contrast, Indigenous Australians had significantly higher rates of bipolar affective disorder and social phobia (current prevalence). Generalisations regarding the risk of psychiatric disorders in Indigenous people cannot therefore be made as this varies by several factors. These include disorder type, sociodemographic factors, Indigenous origin and study method.