HIV has played a key role in TB, modifying its incidence and clinical presentation. This study describes the prevalence of HIV among TB patients attending health facilities in the southern region of Ethiopia. The HIV prevalence was 18% for female and 21% for male TB patients. 15% and 30%, respectively, of the rural and urban patients with TB were HIV positive (p<0.05). 19% (51/261) smear-positive PTB, 26% (36/137) smear-negative PTB and 11% (10/94) of the extrapulmonary TB patients were HIV positive. The proportion of patients with extra-PTB varied from 11% to 38% across the centres and was highest in the zones with the lowest HIV prevalence. In the light of limited diagnostic facilities, clinicians often make a clinical diagnosis of TB without laboratory confirmation. The increase in the number of TB cases could be due to HIV. However, the number of health facilities offering TB treatment in the area also increased (from 53 to 236) during the same period and the increase in TB is likely to be the result of a combination of factors, including improved detection and HIV. It is important to consider this multi-factorial phenomenon when interpreting the increase of TB in a geographical area.