Abstract Objectives Polycystic ovarian syndrome (PCOS) is a heterogeneous endocrine condition that influences 15–20 % of women at their fertile age. In this academic work, we aimed to research serum anti-mullerian hormone (AMH) levels using the Vidas® and Atellica® methods and other hormone parameters in PCOS. Methods This study included 55 controls and 55 PCOS women diagnosed by Rotterdam criteria. AMH levels were measured by Vidas® and the Atellica® devices, and the other parameters were obtained from Ankara Bilkent City Hospital’s Laboratory Information System. Results The AMH levels utilized by the Vidas® (p<0.001) and the Atellica® (p=0.001) were both more elevated in PCOS women. The Vidas® and the Atellica® methods were well correlated, and the correlation coefficient value was 0.899. The AMH cut-off value was 3.23 μg/L with a sensitivity of 65.5 % and a specificity of 34.5 % by utilizing the Vidas® method and 3.66 μg/L with a sensitivity of 65.4 % and a specificity of 36.4 % by utilizing the Atellica® method. PCOS women’s serum AMH levels were positively correlated with fasting glucose and luteinizing hormone (LH) and negatively correlated with age and progesterone. The PCOS group’s levels of serum estradiol (E2) were notably more elevated and levels of serum prolactin were notably lower than the controls. Conclusions This study showed that serum AMH levels measured with both the Atellica® and the Vidas® present significant differences between PCOS patients and the controls but still, AMH alone is not diagnostic enough to distinguish PCOS patients from controls.