ETHNOPHARMACOLOGICAL RELEVANCE: Zanthoxylum capense Thunb. (Rutaceae) is a medicinal plant traditionally used in Mozambique to treat tuberculosis. AIMS OF THE STUDY: The aim of the study was to find antimycobacterial lead compounds from Z. capense. Another goal was to provide scientific validation for the use of this plant in traditional medicine. METHODS AND MATERIALS: By bioassay-guided fractionation, sixteen compounds were isolated and screened for their in vitro antimycobacterial activity against two different strains of M. tuberculosis. Their in vitro cytotoxicity to human THP-1 macrophages was also assessed. The compounds with favourable selectivity index values (SI>10) were further investigated for their ability to inhibit the growth of M. tuberculosis H37Rv in an intracellular macrophage model of infection. RESULTS: The best results were obtained for a benzophenanthridine alkaloid, decarine (1), and an N-isobutylamide, N-isobutyl-(2E,4E)-2,4-tetradecadienamide (15), which showed a high activity against M. tuberculosis H37Rv (MIC of 1.6µg/ml), and a low macrophage cytotoxicity (IC(50)>60µg/ml), indicating considerable selective activity. The benzophenanthridine alkaloid 6-acetonyldihydronitidine (6) revealed cytotoxicity (IC(50) 1.7µg/ml), despite the determined MIC of 6.2-12.5µg/ml. In infected macrophages, decarine (1) was able to reduce bacterial survival by almost two log units at a concentration of 6.2µg/ml 5 days post drug exposure. Compound 15 exhibited an intermediate activity at drug concentrations ranging from 6.2 to 25µg/ml. CONCLUSIONS: The high antimycobacterial activity of decarine found, both in vitro and ex vivo against mycobacteria, and the low cytotoxicity towards human macrophages indicate that it may be valuable as a lead scaffold for the development of anti-TB drugs.