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Objectives The objective of our study was to describe the prevalence of gender diverse (GD) youth among adolescents with polycystic ovary syndrome (PCOS). Methods We conducted a retrospective chart review on patients who met NIH criteria for PCOS in our Multidisciplinary Adolescent PCOS Program (MAPP). We compared those with PCOS to MAPP patients who did not meet PCOS criteria as well as to non-PCOS patients from the Adolescent Specialty Clinic (ASC). Variables analyzed included gender identity, androgen levels, hirsutism scores, and mood disorders. We used chi-square, Fisher’s exact, t-tests, and Wilcoxon rank sum tests to compare groups. Gender identities self-reported as male, fluid/both or nonbinary were pooled into the GD category. Results Within the MAPP, 7.6% (n=12) of PCOS youth self-identified as GD compared to 1.8% (n=3) of non PCOS youth (p=0.01, chi-square). When compared to non-PCOS GD adolescents from ASC (4.4%; n=3), the difference to PCOS youth was no longer significant (p=0.56). Among MAPP patients, gender diversity was associated with higher hirsutism scores (p Conclusions Gender diversity was observed more commonly in those meeting PCOS criteria. PCOS GD youth were more hirsute and reported more depression/anxiety. Routine screening for differences in gender identity in comprehensive adolescent PCOS programs could benefit these patients, as alternate treatment approaches may be desired to support a transmasculine identity.