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Although current evidence suggests increased risk of obesity, insulin resistance, and metabolic alterations in patients with polycystic ovary syndrome (PCOS), especially of a hyperandrogenic phenotype, the impact of each one of these variables on muscle mass remains uncertain. In this case-control study, we evaluated clinical and hormonal characteristics related to lean body mass according to the different PCOS phenotypes. We performed clinical, metabolic, and hormonal assessments and evaluated body compartments by dual-energy X-ray absorptiometry in 133 women of reproductive age. Creatinine served as an indirect marker of lean mass. Median age was 28 (range, 17–37) years. Women with phenotypes A and B (n = 59) had higher body mass index (BMI) and metabolic syndrome prevalence than those with phenotype C (n = 23) and controls (n = 51) (p<0.005). Women with phenotypes A and B also had higher Ferriman-Gallwey score (p<0.001), insulin levels (p = 0.006), HOMA-IR (p = 0.008), testosterone (p = 0.008), free androgen index (FAI) (p<0.001), fat mass index (FMI) (p = 0.015), android-to-gynoid fat ratio (p = 0.036), and bone mineral density (BMD) at lumbar spine (p = 0.027) and total femur (p = 0.013) than controls. Median appendicular lean mass index (ALMI) was higher in phenotypes A and B than in controls (7.01 [IQR, 6.33–8.02] vs. 6.69 [IQR, 5.94–7.09], p = 0.024), but it did not differ significantly from that in phenotype C (6.60 [IQR, 6.16–7.22], p = 0.222). Even after adjusting for BMI, ALMI correlated positively with creatinine in women with phenotypes A and B (rho = 0.319, p = 0.023) but not in those with phenotype C (p = 0.238) or controls (p = 0.097). In multivariate linear regression analyses, ALMI was positively associated with insulin, FAI, FMI, and total femur BMD. The present results suggest that fasting insulin, FAI, fat mass, and total femur BMD were positively associated with increased lean mass in women with PCOS phenotypes A and B. [ABSTRACT FROM AUTHOR]