Background: Patients with Pulmonary tuberculosis (PTB) and hypocholesterolemia have an altered immune function, delayed sputum conversion at two months and increased mortality. However, the assessment for dyslipidemias is not often done in our setting. Methods: A cross-sectional study was conducted among adults at an urban TB clinic in Kampala, Uganda. We included different participants at diagnosis (0), 2, 5, 6 and 8 months of anti-TB treatment. Data was collected from a complete physical examination, a pre-tested structured questionnaire, six-hour fasting lipid profiles and random blood glucose levels. Results: Of the 323 included participants, 63.5% (205/323) were males and the median age was 30 years, IQR (23-39). The prevalence of hypocholesterolemia was 43.65% (95% CI 38.3-49.2). The participants at diagnosis had the highest hypocholesterolemia prevalence, 57.3%, 95% CI (46.7-67.2); and lowest amongst those completing treatment at 6/8 months, 32.2%, 95% CI (21.6-45.2). Significant factors associated with hypocholesterolemia were: male gender (PR 1.52, 95% CI: 1.13-2.03), and duration of anti-TB treatment (0.88, 95% CI: 0.80-0.98). Conclusion: Hypocholesterolemia is common among patients with PTB. The risk of hypocholesterolemia increases with being male and reduces with increased duration of treatment. There is a need for further research in lipid abnormalities in TB patients.