The aim of the present study was to clarify the detailed morphology of efferent and epididymal ducts in adult mice using three-dimensional (3D) analysis. We reconstructed efferent and epididymal ducts in three adult mice using serial paraffin sections and high-performance 3D reconstruction software to draw the core lines of all ducts. By comparing the 3D core lines with the histological features in serial sections, we obtained detailed information on the gross characteristics of the ducts and identified the duct divisions accurately. The intra-testicular rete testis penetrated the tunica albuginea at one place and turned into the extra-testicular rete testis, which branched once or twice to give rise to four efferent ducts within 0.5 mm from the tunica albuginea. As these ducts approached the epididymis, they converged into one again and changed abruptly into the initial segment (IS) of the epididymis. The average length from the tunica albuginea to the IS was 19.7 ± 3.1 mm. In one mouse, we found four additional efferent ducts diverging from the common region with blind ends. The epididymal duct was a single highly convoluted duct with no branch and an average length of 767 ± 26 mm. By dividing the epididymal duct into five regions based on its cytological features and periodic acid-Schiff stainability, we calculated the length and diameter of individual regions accurately. Furthermore, we clearly showed locations of the connective tissue septa that divide the head epididymis into several segments. The epididymal duct followed a complicated, winding path within each segment while drawing a large spiral overall along the circumference of the epididymis. Sometimes the direction of this spiral reversed between adjacent segments. The present study revealed the detailed 3D structures of efferent and epididymal ducts in adult mice.