Purpose Vasoepididymostomy is a technically challenging and complex microsurgical procedure. Recently a new triangulation end-to-side microsurgical technique was reported that allows intussusception of the epididymal tubule into the vasal lumen, resulting in a higher clinical patency rate of 92% with shorter operative time in preliminary clinical studies. We performed a prospective controlled randomized study comparing the patency rate, postoperative sperm granuloma rate and operating time of conventional and intussusception end-to-side vasoepididymostomy in previously vasectomized rats. Materials and Methods We randomized 42, 6-week-old male Wistar rats into 4 groups, including 6 into the sham operation, and 12 each into the control, conventional end-to-side and intussusception end-to-side vasoepididymostomy groups. Bilateral 2-clip vasectomy was performed in all animals except those in the sham operation group. Bilateral intussusception or conventional end-to-side vasoepididymostomy was performed in the assigned animals 2 weeks after vasectomy. Animals in the control group underwent vasectomy only. In the sham operation group the testes were mobilized out of the scrotum and then returned. Rats were sacrificed at 8, 12, 16 and 24 weeks, respectively. The anastomosis and vasectomy sites were inspected for sperm granuloma. To assess patency the abdominal end of the vas was transected and intraluminal fluid was examined microscopically at 400× magnification for the presence of motile sperm. Patency was further confirmed by performing retrograde indigo carmine vasography through the anastomoses. Results In the intussusception and conventional groups the patency rate was 91.7% and 54.2% (p = 0.004), the sperm granuloma rate was 20.8% and 58.4% (p = 0.035), and average operative time was 65.8 and 67.7 minutes (p = 0.197), respectively. Conclusions Intussusception end-to-side vasoepididymostomy is superior to conventional end-to-side vasoepididymostomy with respect to the patency and postoperative sperm granuloma rates. Further investigations are required to confirm such findings clinically in humans.