BACKGROUND: In sub-Saharan Africa, there is a dearth of published literature on extrapulmonary tuberculosis (EPTB). OBJECTIVE: To describe demographic, diagnostic and HIV-status characteristics of patients with EPTB in Bénin, their treatment outcomes, and among those who completed their treatment in the Centre National Hospitalier de Pneumo-Phtisiologie (CNHP-P), the proportion whose bodyweight increased during treatment. MATERIAL AND FINDINGS: This was a retrospective cohort study with comparisons made between EPTB and new smear-positive pulmonary tuberculosis (NPTB) patients diagnosed in the country from January to December 2011. There were 383 EPTB patients (9% of all TB cases) with a mean age of 35 years, male/female ratio of 1.3 and important regional variation. There were significantly more females (p = 0.001), children <15 years (p<0.001) and HIV-positive patients (p = 0.005) with EPTB compared with NPTB. Pleural effusion, spinal and lymph node tuberculosis accounted for 66% of all EPTB. Children <15 years represented 16% of cases, with lymph node disease being most common among them (p<0.001). Of 130 EPTB patients registered in CNHP-P, 7% had a confirmed bacteriological/histological diagnosis. There were 331 (86%) patients who successfully completed treatment. More patients with EPTB were lost-to-follow-up compared with NPTB (p<0.001) with all these patients from one region. The best treatment completion rates were in children <15 years (OR:3.5, 95%CI:1.0-14.8) while patients with pleural effusion and ascites had the worst outcomes. Of 72 HIV-coinfected patients, 88% were on antiretroviral therapy (ART). HIV-positive status was associated with poor outcomes while those on ART fared better. In the CNHP-P, more than 80% who completed their treatment showed an increase in bodyweight and this was more evident in HIV-positive compared with HIV-negative patients (p = 0.03). CONCLUSION: Patients with EPTB generally do well in Bénin, although the TB Programme would benefit through more attention to accurate diagnosis and earlier start of ART in HIV-infected patients.