We aimed to investigate whether overweight/obesity is associated with omentin and chemerin. The study group consisted of 81 women with Polycystic ovarian syndrome (PCOS) (41 lean, BMI < 25 kg/m² and 40 overweight or obese, BMI > 25 kg/m²) and 61 healthy subjects (31 lean, BMI < 25 kg/m² and 30 overweight or obese, BMI > 25 kg/m²; control group). The clinical, endocrine, metabolic parameters, plasma omentin and chemerin levels were measured in patients and compared to control. In all subjects with PCOS (n = 80), serum chemerin levels were higher compared with those of the controls (n = 58) (7.71 ± 1.78 ng/mL versus 6.94 ± 0.82 ng/mL, p = 0.003). However, serum omentin levels were not significantly different between the PCOS subjects and the controls (1.55 ± 0.43 ng/mL versus 1.69 ± 0.37 ng/mL, p = 0.056). The mean chemerin concentrations were significantly elevated in the obese PCOS group compared with the obese control subjects (8.98 ± 1.45 ng/mL versus 7.02 ± 0.67 ng/mL, p = 0.000) and the nonobese PCOS group compared with the obese control subjects (6.57 ± 1.17 ng/mL versus 7.02 ± 0.67 ng/mL, p = 0.000). In conclusion, fat mass seems to be the main determinant factor of increased chemerin and decreased omentin in women with PCOS.