A 30-year-old man was referred to our hospital with a complaint of male infertility, presenting abnormal semen analysis (semen volume 0.1 ml, sperm concentration 1.2 x 10(6)/ml, sperm motility 0%). Radiological examinations demonstrated right renal agenesis and a cystic mass extending from the prostate to the posterior of the bladder. Our final diagnosis was obstruction of the ejaculatory duct secondary to right ectopic ureter associated with ipsilateral renal agenesis. The patient was treated by transurethral unroofing of the cyst. Three months after the surgery, the cystic mass disappeared and the seminal findings showed marked improvement.