Understanding mental health issues facing individuals with disorders/differences of sex development (DSD) is crucial for optimizing evidence-based practices in this population. To compare the prevalence of psychiatric diagnoses among patients diagnosed with complete androgen insensitivity syndrome (CAIS) or Müllerian duct aplasia/agenesis (MA) to male and female reference groups. Retrospective cohort study. Three large integrated health systems. All individuals with confirmed CAIS or MA enrolled in one of three Kaiser Permanente healthcare systems between January 1, 1988, and January 31, 2017. For each DSD patient, age-, race/ethnicity- and health system-matched male and female referents with typical sex development were randomly selected. Mental health diagnoses and use of psychiatric medications. The prevalence of anxiety and depressive disorders in the CAIS and MA cohorts was approximately twice as high as in male referents without DSD, but the corresponding differences relative to female referents were less evident. A subgroup of MA patients with uterine agenesis had higher prevalence of bipolar disorder than either reference group, but these results were accompanied by wide confidence intervals. Women with CAIS and MA more frequently filled psychiatric medications compared to male but not female referents. On balance, these findings are reassuring, albeit requiring confirmation in other settings. Future studies using longitudinal designs and patient-reported outcomes are needed to evaluate changes in mental health status of CAIS and MA patients at different ages and different intervals following initial diagnosis.