Brachylaima mazzantii (Travassos, 1927) is known only from its original description. Until now, no attempt has been made to address the morphology of this species by means of modern microscopy techniques. In the present study, the information generated on the anatomy of B. mazzantii allowed the re-examination of the morphology of this species. The most significant new data is related to the terminal genitalia. The detailed analysis of the reproductive system of this species evidenced the presence of a seminal vesicle external to the cirrus pouch which contains a short unarmed cirrus, and also the presence of a well developed metraterm and gland cells in the genital atrium. The results also revealed some traits concerning other systems, previously unnoticed, including the shape and relative position of the excretory vesicle and the tegument ornamentation. The main advantage of using confocal microscopy to study the morphology of digeneans is the fact that with only one technique it is possible to examine the gross anatomy, cell morphology and surface topography. Confocal tomographies show much more detail than light microscopy images, and allow getting information on cell morphology, usually achieved only by histological techniques, along with some information on tegument ornamentation, usually obtained through scanning electron microscopy. The accumulation of information on the morphology of different digenean species through confocal microscopy will allow future comparative studies, which may ultimately contribute to the better resolution of the systematics of this group.