Tuberculosis (TB) is a major cause of human mortality particularly in association with the human immunodeficiency virus (HIV). spp. has emerged as an opportunistic infection especially in HIV patients. The high prevalence of TB and HIV coupled with the lack of a definitive laboratory diagnosis for spp. could lead to misdiagnosed pulmonary TB. This study determined the prevalence of pulmonary infections due to spp. and in sputum of HIV and non-HIV patients with suspected pulmonary tuberculosis at KATH. A total of sixty sputum samples were obtained from HIV and non-HIV patients with suspected pulmonary tuberculosis. Samples were examined by fluorescence based Ziehl-Neelsen staining, culture, and PCR methods. The prevalence of spp. and was 18.3% and 20%, respectively, with the latter having the highest rate among patients aged 21-40 years (=0.075). The prevalence of spp. among HIV patients was 90.9% whilst 16.7% of the patients had HIV/ spp. coinfection. Detection of by fluorescence-based Ziehl-Neelsen staining, culture, and PCR yielded 9 (15%), 11 (18.3%), and 12 (20%), respectively. There is a high prevalence of nocardiosis especially in HIV patients. PCR is a better diagnostic method that detects both spp. and and should be incorporated into routine diagnosis for pulmonary infections.