The purpose of this study was to examine the effects of baseline ovarian cysts on the clinical response to controlled ovarian hyperstimulation (COH) in an in vitro fertilization (IVF) program. Patients were divided into two groups: group 1 (n = 21) had cysts with mean diameters between 10 and 45 mm on their baseline ultrasound before COH, and group 2 (n = 76) had no ovarian cysts on their baseline ultrasound. There was no statistically significant difference between the groups in maximum serum estradiol, the number of follicles greater than or equal to 10 mm on the day of human chorionic gonadotropin (hCG) injection, the number of follicles greater than or equal to 15 mm on the day of hCG injection, the number of oocytes retrieved, and the number of embryos transferred. There was no difference between the groups in the cycle cancellation rate, in the pregnancy rate per cycle, or in the pregnancy rate per embryo transfer. This study suggests that small baseline ovarian cysts do not negatively impact on ovulation induction parameters or pregnancy rates in an IVF program.