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Objective: To determine clinical pattern, prevalence, and factors associated with pediatric immune reconstitution inflammatory syndrome (IRIS) in Uganda., Design: A prospective, multicenter cross-sectional study., Methods: We enrolled HIV-infected children receiving antiretroviral therapy (ART) between 0.5 and 6 months duration from December 2006 to October 2007 at three pediatric clinics in Uganda. Children were evaluated for IRIS at a one-time study visit by a standardized pediatric case definition., Results: The IRIS prevalence was 38% [95% confidence interval (CI) 31-46] among 162 children (57% female) with a median age of 6 years (interquartile range 2.5-11 years). Of the IRIS events, 77% were unmasking of a new opportunistic infection and 23% were probable paradoxical IRIS events toward prior opportunistic infections. The majority of IRIS events (55%) occurred in the first month of ART. The clinical events were diverse, with tuberculosis-IRIS (29%) being the most frequent presentation. Independent risk factors for IRIS were pre-ART CD4(+) cell percentage below 15% (odds ratio = 3.1, 95% CI 1.2-8.4, P = 0.027), current CD8(+) cell absolute count below 1000 cells/microl (odds ratio = 4.3, 95% CI 1.8-10.4, P = 0.001), male sex (odds ratio = 2.6, 95% CI 1.06-8.4, P = 0.01), and a cough of more than 1 week duration at the current clinic visit (odds ratio = 4.3, 95% CI 1.7-10.7, P = 0.002). A more than 25 CD4(+) T-cells increase at current study visit from the pre-ART baseline was associated with IRIS by univariate (P = 0.005) but not multivariate analysis., Conclusion: IRIS events commonly occur early after ART initiation in children with advanced immunosuppression, as commonly seen in resource-limited areas. Both healthcare providers and caregivers of the children need awareness of IRIS to minimize ART nonadherence.