Journal of Tuberculosis Research, 2017, 5, 189-200 Background: In Benin, little is known about the influence of both gender and HIV-status on diagnostic patterns and treatment outcomes of Tuberculosis (TB) patients. Objective: To assess whether differences in gender and HIV status affect diagnostic patterns and treatment outcomes of TB patients. Methods: Retrospective cohort study of patients registered in 2013 and 2014 in the three largest TB Basic Management Units in south Benin. Results: Of 2694 registered TB patients, 1700 (63.1%) were male. Case notification rates were higher in males compared with females (96 vs 53/100,000 inhabitants). The male to female ratio was 1:1 in HIV positive patients, but was 2:1 among HIV negative cases. In HIV-positive patients, there were no differences in TB types between men and women. In HIV-negative patients, there were significantly higher proportions of females with clinically diagnosed pulmonary TB (p = 0.04) and extrapulmonary TB (p < 0.001). Retreatment TB was 4.65 times higher amongst males compared with females. For New bacteriologically confirmed pulmonary TB, no differences were observed in treatment outcomes between genders in the HIV positive group; but significantly more unfavorable outcomes were reported among HIV negative males, with higher rates of failure (p < 0.001) and loss-to-follow up (p = 0.02). Conclusion: The study has shown that overall TB notification rates were higher in males than in females in south Benin, with more females co-infected with HIV. Unfavorable outcomes were more common in HIV-negative males.