Background Adipokines have been suggested to play an important role in the pathogenesis of polycystic ovarian syndrome (PCOS). Omentin is an adipokine secreted essentially by visceral adipose tissue with an insulin-sensitizing effect. Insulin resistance (IR) is a common feature of PCOS, therefore the aim of this study was to investigate omentin-1 level in adolescent girls with PCOS and its relationship with IR and androgens. Method A total of 41 obese girls with PCOS, and 30 age- and body mass index (BMI)-matched obese girls without PCOS were enrolled in the study. The demographic, clinic and laboratory characteristics of the groups were compared. Additionally, bivariate correlation analysis of omentin-1 with BMI standard deviation score (BMI-SDS), insulin, glucose, homeostatic model assessment of IR (HOMA-IR), total and free testosterone was performed. Results In the PCOS group HOMA-IR, free and total testosterone were higher than in the control group. Omentin-1 was lower in the PCOS group compared with the controls (55.01 +/- 7.99 ng/mL vs 59.10 +/- 7.02 ng/mL, respectively; P = 0.027). Omentin-1 was inversely correlated with free testosterone (r = -0.527, P = 0.030) and BMI-SDS (r = -0.241, P = 0.046) but it was not correlated with total testosterone, HOMA-IR, glucose, insulin or serum lipids. Conclusion Omentin-1 was lower in obese girls with PCOS and hyperandrogenism was associated with this condition.