This study aims to assess ovarian reserve markers in Behçet's disease (BD) patients. Ten BD and 22 healthy controls were evaluated for ovarian reserve by examining the levels of follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol, inhibin B, total morning testosterone, prolactin, thyroid-stimulating hormone (TSH), and antral follicle count. Anti-Müllerian hormone (AMH) was measured using two different enzyme-linked immunosorbent assay (ELISA) kits. Demographic data, menstrual abnormalities, disease parameters, and treatments were also analyzed. The median current age was similar in BD patients and controls (34 (20-40) vs. 31.3 (20-42) years, p = 0.33). A positive correlation was observed between the AMH Gen II ELISA and AMH/MISAnshLabs ELISA assays in the BD patients (r = +0.98; p < 0.0001) and healthy controls (r = +0.93; p < 0.0001). The mean AMH by Gen II (0.93 ± 0.8 vs. 2.59 ± 1.8 ng/mL, p = 0.01) and AMH/MIS AnshLabs ELISA (1.07 ± 0.86 vs. 2.51 ± 1.8 ng/mL, p = 0.02) were significantly reduced in the BD patients versus controls. A trend of decreased AMH (<1.0 ng/mL) was observed in BD patients compared to that in the controls (50 vs. 19 %, p = 0.09) using either kits. The mean FSH was significantly higher in the BD patients compared to that in the controls (9.1 ± 3.6 vs. 6.5 ± 2.7, p = 0.04). No differences were found for the other ovarian parameters in both groups (p > 0.05). Current disease activity was only observed in BD patients with a low AMH level; however, there was no statistical significance (40 vs. 0 %, p = 0.44). Cyclophosphamide use was reported in only one patient with a low AMH and high FSH level. The present study was the first to suggest that BD patients may have diminished ovarian reserve. The contribution of disease activity remains to be determined.