During a period of eight months, the carcases of 16,800 slaughter cattle were inspected at a city abattoir in Uganda. Eighty-seven of them had tuberculosis-like lesions and tissue samples were cultured. Only 17 cultures yielded acid-fast bacilli; 11 of them were confirmed as Mycobacterium bovis and six as non-tuberculous mycobacteria (NTM). GenoType Mycobacterium assays on the six NTM identified two as Mycobacterium fortuitum and one as Mycobacterium intracellulare, but three were unidentified. Characterisation of the M bovis isolates by spoligotyping and IS6110 restriction fragment length polymorphism (RFLP) revealed that five of the six spoligotype patterns observed in the 11 strains had not been previously reported, and seven of the nine isolates typed by RFLP had multicopy number IS6110 patterns. Six of the 11 infected carcases had multiple sites of infection, but none was condemned as unfit for human consumption.