To investigate whether the variable length of the epididymis in men with congenital bilateral absence of the vas deferens (CBAVD) might have a correlation with fertilization and pregnancy rates in in vitro fertilization (IVF) treatment, we conducted a retrospective study involving a total of 60 CBAVD patients. All patients in this study had epididymal micropuncture in conjunction with perivascular nerve stimulation as part of the IVF program at the Nagoya University Hospital Reproduction Center. The patients were classified into 3 groups: group I consisted of patients having only a proximal portion of the caput epididymidis with a length of between 0.5 and 1.9 cm, group II consisted of patients with the caput and a portion of the corpus epididymidis with a length of between 2.0 and 4.0 cm, and group III consisted of patients with the caput, corpus and cauda of the epididymis measuring more than 4.0 cm. There were no differences in the sperm count, progression and normal morphology among the 3 groups; however, the motility was progressively higher in patients with a longer epididymis (12% in group 1, 18% in group II and 31% in group III). It was evident that group III showed the highest fertilization and pregnancy rate per patient (23% and 28%, respectively) among the 3 groups. This study shows that epididymal sperm from CBAVD patients with a longer epididymis have a higher IVF rate than CBAVD patients with a shorter epididymis.