Classical schemes of the adult Schistosoma mansoni reproductive system have been described. In our study, whole adult worms derived from unisexual or mixed infections and stained with carmine chlorine were virtually and tomographically analyzed under confocal laser scanning microscopy. We found that: (1) there were morphological differences in the ovary, vitteline glands and testicular lobes between specimens derived from unisexual or mixed infections; (2) there was always a single lobed ovary (three or four lobes), presenting differentiation from the anterior to the posterior lobes, where the most mature oocytes were located; (3) the proximal segment of oviduct was connected to an ampullary dilatation, full of tailed spermatozoa, characterizing a seminal receptacle; (4) there was no long vitelline duct, but a short one that begins at the end of the proximal region of the vitelline gland; (5) long cells of Mehlis' gland placed radially around the ootype were not observed. Otherwise, the ootype was only lined by thick cuboidal epithelial cells with plaited bases and nuclei with flabby chromatin, making a clear distinction from the uterine epithelium. This morphological feature suggests that each cell represents a gland. (6) In coupled males, the specimens located inside the gynaecophoric canal had smaller testicular lobes, suckers, and body length and width when compared to their partners. Our results show that the reproductive system does not follow a unique pattern within flatworms. Due to its better resolution, confocal laser scanning microscopy, using a reflected mode with tomographic sections, allows new interpretations, modifying the adopted and current descriptions of the internal morphological structures of S. mansoni adult worms.