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Background Infertility is a global concern in both humans and domestic animals, with male factors accounting for nearly half of all cases. Among male reproductive structures, the efferent ductules play a crucial but understudied role in fertility. These tubules connect the testis to the epididymis and are primarily responsible for luminal fluid reabsorption, a process essential for sperm concentration, maturation, and transport. This study aimed to provide a comparative morphological and histological characterization of the efferent ductules in four species—rats, bulls, stallions, and boars—focusing on regional variations (proximal, middle, and distal) and their potential functional implications. Results Gross dissection and histological evaluation revealed a columnar epithelium composed of ciliated and nonciliated cells in all species. Comparative analysis identified species-specific differences in connective tissue composition, smooth muscle thickness, and epithelial dimensions. Proximal regions generally exhibited larger lumen diameters and lower epithelial heights, whereas distal regions showed increased ciliary height and, in some species, a greater presence of cytoplasmic granules, suggesting enhanced secretory or absorptive activity prior to sperm entry into the epididymis. Boars exhibited a particularly thick smooth muscle layer and abundant granules in the distal region. Morphometric measurements supported these observations, demonstrating consistent patterns of structural variation across species. Conclusions The efferent ductules display complex, species-specific architecture and specialized regional features that likely contribute to their functional role in fluid reabsorption and sperm modification. These findings expand current knowledge of male reproductive morphology in domestic animals and highlight the need for further functional studies beyond rodent models to better understand fertility regulation in veterinary species.