Objective: To determine the prevalence of fungal pathogens in patients with pulmonary tuberculosis at Mbagathi District Hospital TB clinic. Design: One hundred and seventy two sputum samples were collected from patients who were confirmed to have pulmonary tuberculosis at Mbagathi District Hospital TB clinic. These samples were subjected to mycological investigation using microscopy and culture. Results: Pulmonary fungal pathogens were isolated as co-pathogens with Mycobacterium tuberculosis in 76 (44.18%). Yeasts accounted for 46/172 (26.7%), with 33/172 (19%) being Candida albicans, 3/172 (1.7%) were identified as Candida dubliniensis, 1/172 (0.6%) was Candida guilliermondii, while 3/172(1.7%) were Candida tropicalis. Cryptococcus laurentii was isolated in 2/172 (1.2%). Colonization of Mycobacterium tuberculosis with moulds was as follows: 2/172 (1.2%) Aspergillus flavus, 3/172 (1.7%) Aspergillus fumigatus 4/172 (2.3%) Aspergillus niger, 2/172 (1.2%) Scytalidium hyalinum and 4/172 (2.3%) Trichosporon asahii. Pneumocystis jirovencii oocysts were positive in 19/172 (11.0%) on Toluidine O blue. Gram stain of the sputum samples yielded: 4/172 (2.3%) Gram negative rods, 10/172 (5.8%) Gram positive cocci and 6/172(3.5%) Gram positive rods. Conclusion: Pathogenic fungi and other bacterial pathogens may be significant co-infecting pathogens complicating the management of TB. Clinicians in Kenya should be aware of co-infection of Mycobacterium tuberculosis with opportunistic pulmonary fungal and bacterial pathogens. HIV infection is a significant pre-disposition to pulmonary tuberculosis. The two conditions present severe immunosuppression. Confounded by prolonged TB treatment, this group represents a high risk for acquiring opportunistic fungal pathogens.