BACKGROUND: In high tuberculosis (TB) burden countries, a significant proportion of the latent TB reservoir is established by the age 5 years. There are critical knowledge gaps in our understanding of the age-specific prevalence of TB infection and the influence of HIV exposure on TB infection in the first 5 years of life among HIV-uninfected children in sub-Saharan Africa. METHODS: We measured TB infection with the Quantiferon Gold-in-Tube (QFT) and tuberculin skin tests (TST) in 447 children ≤60 months and their 284 HIV-infected and IV-uninfected mothers in rural Uganda. RESULTS: The overall prevalence of TB infection in children ≤60 months by TST was 24% (95% confidence intervals [CI]: 19.9-27.9). The prevalence of TST positivity was highest among children in their first year of life (36%; 95% CI: 26.0-45.9) and declined with age to 19% at 36-60 months of age, χ test for trend P = 0.014. In contrast, 4% (95% CI: 1.9-5.87%) of children had a positive QFT, and there was no trend detected with age, P = 0.576. QFT positivity was detected as early as 5 months. HIV-exposed uninfected children had significantly higher odds of TB infection by QFT (odds ratio [OR]: 21.2; P = 0.008; 95% CI: 2.2-204.7) or positive TST or QFT (OR, 2.4; P = 0.020; 95% CI: 1.2-5.1) compared with HIV-unexposed uninfected children, adjusting for age, BCG vaccination and a positive maternal TST or QFT. CONCLUSIONS: An appreciable prevalence of TB infection was detected in early childhood. HIV-exposed uninfected children have a higher risk for TB infection compared with children born to HIV-uninfected mothers.