As epididymal sperm (EP) are not exposed to seminal plasma, they are physiologically different from ejaculated spermatozoa (EJ). Therefore, the aim of this study was to morphologically characterize the head of EP recovered from the epididymis tail, and to evaluate if the physiological differences between EP and EJ were also expressed in the head’s shape and size. EP and EJ were recovered from seven Gir bulls and were individually assessed. Sperm cells were washed, fixed, and 20 cells from each animal were analyzed by atomic force microscopy (AFM). The images were acquired through contact mode. Then, an off-line processing software was used and the images acquired were manually segmented using digital zoom of the original images. Twenty-four structural features were assessed including one, two, and three dimensional parameters, and also shape descriptors which were calculated based on the one and two dimensional parameters. Data were compared by t-test, then, a collective analysis was performed using principal component analysis (PCA). The EP group presented higher roughness and elongation (P ≤ 0.05), and smaller form factor and circularity rate than that of the EJ group (P ≤ 0.05). For the other parameters no differences (P ≥ 0.05) were observed. In addition, in the PCA analysis no differences among EP and EJ were observed either (P ≤ 0.05). This study showed that EP and EJ collected from the same sire presented similar characteristics in nineteen of the twenty-four parameters evaluated, indicating that absence of seminal plasma does not affect the morphology of EP.