Anti-Müllerian hormone (AMH) is commonly used as a marker of ovarian reserve. Although obesity is associated with decreased fertility, the relationship between body mass index (BMI) and AMH remains uncertain, hindering the accurate interpretation of AMH. We sought to assess the relationship between serum AMH and BMI in patients with and without polycystic ovarian syndrome (PCOS). This study analysed 500 patients at a single centre between 2020 and 2021. Patients were divided into cohorts: those with BMI 40 kg/m . Patients with and without PCOS were included. Chi-square tests, Fisher’s exact tests, multiple linear regression analysis and independent t-tests were performed as appropriate. In the general study population, serum AMH was not significantly different in the BMI >40 kg/m group compared to the BMI <40 kg/m group (4.3 ± 5.6 vs. 4.3 ± 5.6, p = .35). Patient ages between these two groups differed, with an average age of 35.4 ± 5.4 years in the BMI <40 kg/m group and 33.7 ± 5.4 years in the BMI <40 kg/m group (p = .031). Our multivariate regression analysis, which adjusted for age, demonstrated a significant interaction effect between BMI and PCOS diagnosis, indicating that the relationship between BMI and AMH is dependent on PCOS status (β = -.03, 95% confidence interval [CI]: -0.05, 0.00, p = .044). In patients without PCOS, we found a non-significant relationship between AMH and BMI (β = .00, 95% CI -0.01, 0.01, p = .7); however, in patients with PCOS, AMH significantly decreased as BMI increased (β = -.03, 95% CI -0.06, 0.00, p = .034). BMI has an inverse association with AMH levels in patients with PCOS, indicating a need for future research to determine if that interaction represents a clinically significant negative effect on reproductive function.© 2023 The Authors. Clinical Obesity published by John Wiley & Sons Ltd on behalf of World Obesity Federation.