Objective Obesity may reduce sertoli cell functions in men. The aim of the study was to investigate antimullerian hormone (AMH) and inhibin B levels (sertoli cell markers) in obese boys and their relations to cardiovascular risk factors such as insulin sensitivity index, aortic intima media thickness (aIMT) and high sensitive c-reactive protein (hsCRP). Patients, methods 121 obese and 38 healthy lean adolescents were included in the study. Serum AMH, inhibin B, gonadotropins, total testosterone, lipids, hsCRP, glucose and insulin levels were detected and analyzed. Insulin resistance was analyzed using the homeostasis model assessment (HOMA-IR). aIMT was measured by high-resolution B-mode ultrasonography. Results Serum AMH, inhibin B and total testosterone levels were lower in the obese adolescents (p = 0.01, p = 0.009 and p = 0.002, respectively). aIMT measurements (p < 0.001, 0.630.09 and 0.47 +/- 0.06 mm, respectively) and hsCRP levels (p < 0.001, 2.5 +/- 0.4 and 0.66 +/- 0.69 mg/L, respectively) were significantly increased in the obese group. Obese with IR group had decreased AMH levels (p = 0.02, 53.0 +/- 20.5 and 66.7 +/- 19.5 ng/mL, respectively) and increased triglycerides, HOMA-IR, aIMT measurements than non-IR obese group. AMH levels were correlated negatively with body mass index (r: - 0.108, p = 0.03), HOMA-IR (r: - 0.358, p = 0.003) and fasting insulin levels (r: - 0.389, p = 0.001) in obese group with IR. Conclusion We found that concentrations of both sertoli cell markers (AMH and inhibin B) were significantly lower in obese pubertal boys especially in obese with IR. Obesity and IR might be important factors for the sertoli cell impairment in pubertal boys.