Background Reproduction is a vital necessity for effective livestock production, and its productivity depends on the normal structure and function of the genital organs. Methods A study was carried out to characterize gross pathological lesions and identify aerobic bacteria from reproductive organ disorders of slaughtered she-camels ( Camelus dromedarius ) in the Fafen zone of the Somali Regional States of Ethiopia. All the available reproductive organ (50) samples were considered during sampling and cultured bacteriologically using a standard procedure. Results Accordingly, eighteen out of fifty female dromedary camels (36%, 18/50) were found to have gross pathological lesions on the genitalia, including acute metritis (10%), pyometra (8%), cervicitis (6%), vaginitis (4%), follicular cysts (4%), inactive/hypoplastic ovaries (2%) and vaginal lymphocytic masses (2%). Based on the anatomical distribution of reproductive tract lesions, uterine abnormalities were the most frequently observed lesions (18%, 9/50), followed by cervicovaginal abnormalities (12%, 6/50) and ovarian abnormalities (6%, 3/50). In addition, eight different species of bacteria were identified from the sampled reproductive organs: 29 (58%) from the uterus, 7 (14%) from the cervix, 7 (14%) from the vagina, 4 (8%) from the udder, and 3 (6%) from the ovary. Of the total isolated bacteria, coagulase-negative Staphylococcus species 25 (50%), Staphylococcus aureus 18 (36%), E. coli 12 (24%), Streptococcus species 11 (22%), Salmonella species 6 (12%), Proteus species 8 (16%), Shigella species 2 (4%) and Klebsiella species 1 (2%) were the most commonly identified bacterial species. Conclusion The study revealed that gross lesions of reproductive tracts and their bacterial isolates are prevalent in female dromedary camels. The role of each reproductive tract lesion and bacterial isolate as causes of reproductive failure in camels requires further investigation.