We encountered an unexpectedly high rate of ovarian cysts in premenopausal women receiving sirolimus and tacrolimus following islet transplantation. The goal of this retrospective chart review was to determine the frequency of ovarian cysts found on pelvic ultrasound examinations of female islet transplant recipients and to look for potential causal factors. Fifty-seven women with a median age of 42.5 years underwent islet transplantation at the University of Alberta. Ovarian cysts were found in 31 out of 44 (70.5%) premenopausal and two out of 13 (15.4%) postmenopausal women (P = 0.001). No women using combined oral contraception developed ovarian cysts. Eight women required surgery; in four women undergoing cystectomy or unilateral oophorectomy, ovarian cysts recurred. Sirolimus withdrawal was associated with a reduction in cyst size and resolution of cysts in 80% of subjects. The risk of ovarian cysts should be discussed with female islet transplant candidates and pelvic ultrasounds performed routinely post-transplant.