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Background  Antiretroviral therapy (ART) effectively decreases tuberculosis (TB) incidence long-term, but is associated with high TB incidence rates in the first 6 months. We sought to determine the incidence and the long-term effects of TB during ART on HIV treatment outcome, and the risk factors for incident TB during ART in a large urban HIV clinic in Uganda.    Methodology/Principal Findings  Routinely collected longitudinal clinical data from all patients initiated on first-line ART was retrospectively analysed. 5,982 patients were included with a median baseline CD4+ T cell count (CD4 count) of 117 cells/mm 3  (interquartile range [IQR]; 42, 182). In the first 2 years, there were 336 (5.6%) incident TB events in 10,710 person-years (py) of follow-up (3.14 cases/100pyar [95% CI 2.82–3.49]); incidence rates at 0–3, 3–6, 6–12 and 12–24 months were 11.25 (9.58–13.21), 6.27 (4.99–7.87), 2.47 (1.87–3.36) and 1.02 (0.80–1.31), respectively. Incident TB during ART was independently associated with baseline CD4 count of <50 cells/mm 3  (hazard ratio [HR] 1.84 [1.25–2.70],  P  = 0.002) and male gender (HR 1.68 [1.34–2.11],  P <0.001). After two years on ART, the patients who had developed TB in the first 12 months had a significantly lower median CD4 count increase (184 cells/mm 3  [IQR; 107, 258, n = 118] vs 209 cells/mm 3  [124, 309, n = 2166],  P  = 0.01), a larger proportion of suboptimal immune reconstitution according to two definitions (increase in CD4 count <200 cells/mm 3 : 57.4% vs 46.9%,  P  = 0.03, and absolute CD4 count <200 cells/mm 3 : 30.4 vs 19.9%,  P  = 0.006), and a higher percentage of immunological failure according to the WHO criteria (13.6% vs 6.5%,  P  = 0.003). Incident TB during ART was independently associated with poor CD4 count recovery and fulfilling WHO immunogical failure definitions.    Conclusions/Significance  Incident TB during ART occurs most often within 3 months and in patients with CD4 counts less than 50 cells/mm 3 . Incident TB during ART is associated with long-term impairment in immune recovery.

Incident Tuberculosis during Antiretroviral Therapy Contributes to Suboptimal Immune Reconstitution in a Large Urban HIV Clinic in Sub-Saharan Africa