To evaluate the effect of prolonged Gonadotropin releasing hormone (GnRH) agonist downregulation in patients with endometriomas of less than 5 cm on the outcome of the proceeding Intracytoplasmic sperm injection (ICSI) trial. In a randomized controlled trial at a university teaching hospital, 90 patients indicated for ICSI and having unilateral single endometrioma of less than 5 cm in diameter were randomized into 2 groups. Group A (45 patients) received the standard long protocol; whereas group B (45 patients) received 3 consecutive Intramuscular (IM) injections of triptorelin 3.75 mg 28 days apart followed by the standard long protocol 28 days after the last injection. There were no significant differences in the clinical and hormonal characteristics between the 2 groups. All ICSI cycle characteristics including number of retrieved oocytes, fertilized oocytes, and transferred embryos were also not significantly different. However, patients who received prolonged GnRH agonist therapy showed significantly higher chemical ( P = .011), clinical ( P = .018), and ongoing ( P = .028) pregnancy rates. Prolonged GnRH agonist downregulation improves the pregnancy rates in patients with small endometriomas undergoing ICSI.