Purpose The aim of this study was to determine the autoimmune effects of ankylosing spondylitis (AS) on the fertility potential of women by evaluating ovarian reserves of AS patients. Methods A total of 104 patients, 52 in the AS group (study group) and 52 in the control group were included in the study. Ovarian reserve was evaluated by serum anti-Mullerian hormone (AMH) levels, antral follicle count (AFC) and baseline serum follicle-stimulating hormone (FSH) levels. Results The mean serum AMH levels were significantly lower in the study group when compared to the controls (2.203 +/- 1.110 vs. 1.188 +/- 0.891,p < 0.001). In addition, the mean AFC was also significantly lower in the study group. (10.67 +/- 1.81 vs. 9.54 +/- 2.50,p = 0.009). Mean FSH levels were calculated to be 6.72 +/- 1.14 in the study group and 7.21 +/- 1.22 in the control group. The difference was not statistically significant (p = 0.781). Conclusion This study shows that AS like several other autoimmune conditions has an adverse effect on the female fertility potential. Therefore, an early start and long-term management of AS patients who have fertility desire is recommended. Serum AMH levels can be used in monitoring ovarian reserve and in early detection of reproductive decline of AS patients. ClinicalTrial Number NCT04209881.