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Suboptimal response to antiretroviral therapy (ART) is common among children living with HIV (CLHIV) in resource-limited settings. We sought to assess virologic failure (VF), time for switching to second-line regimens and factors associated with VF in CLHIV receiving first-line ART in Cameroon.An observational cohort study was conducted in 375 CLHIV initiating a first-line ART and treated for ≥6 months at the National Social Insurance Fund Hospital in Yaoundé-Cameroon from 2009 to 2013. Using logistic regression, predictors of VF and delayed switch were assessed by univariate and multivariate analysis. P < 0.05 was considered statistically significant.Overall, 17% (64/375) CLHIV experienced VF on first-line ART after a median time of 28 (interquartile range: 22–38) months. After VF, median time to switching from first- to second-line ART was 20 (interquartile range: 8–24) months. In multivariate analysis, VF was associated with male gender (adjusted odds ratio: 0.36; 95% confidence interval: 0.19–0.71; P = 0.003), motherless children (adjusted odds ratio: 2.9; 95% confidence interval: 1.3–6.06; P = 0.005) and treatment with stavudine-containing compared with zidovudine-containing regimens (P = 0.022). Overall, male gender, orphanhood (motherless) and treatment with stavudine-containing regimens predicted VF at a rate of 70% (area under curve =0.70).VF on first-line pediatric ART is common, and switching children failing first-line to second-line ART is considerably delayed. These results suggest performance of pediatric ART program can be improved by targeting orphans, adapting counseling for male children, complete phasing-out of stavudine and ensuring timely switch to second-line regimens.