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Pediatric human immunodeficiency virus (HIV) infection and malnutrition are still 2 major health issues in sub-Saharan Africa including Burkina Faso where few studies have been conducted on child malnutrition and HIV infection. This study assessed the effects of antiretroviral therapy (ART) in HIV infection and also compared the prevalence of malnutrition in terms of an inadequate diet, underweight, stunting, and wasting among HIV-infected and uninfected children less than 5 years in Bobo-Dioulasso city, Burkina Faso.This was a case–control study matching for age and sex in 164 HIV-infected and 164 HIV-uninfected children. The sociodemographic characteristics of mothers and children, household food security, drinking water source, child feeding and care practices, and child anthropometric data such as body weight, height, and mid-upper arm circumference were collected.The prevalence of food insecurity and inadequate diet was 58% and 92% of children less than 5 years of age, respectively. The prevalence of underweight, stunting, and wasting was 77% versus 35%, 65% versus 61%, and 63% versus 26% in HIV-infected and uninfected children less than 5 years of age, respectively. Out of 164 HIV-infected children, 59% were on ART initiation during data collection and the median of CD4 cell counts was 1078 cells/μL. HIV-infected children on ART had greater CD4 cell counts (P = .04) and higher weight-for-age Z (P = .01) and weight-for-height Z scores (P = .03) than those without ART. HIV infection was a risk factor for those who had inadequate dietary intake [adjusted odds ratio (AOR) = 2.17, 95% confidence interval (CI) 1.17–3.62, P = .04]. In addition, HIV-infected children were more likely of being underweight (AOR = 10.24, 95% CI 4.34–24.17, P < 0.001) and wasting (AOR = 5.57, 95% CI 2.49–12.46, P < 0.001) than HIV-uninfected children less than 5 years of age.High prevalence of malnutrition was observed in HIV-infected children compared with HIV-uninfected children. Except for ART, nutritional assessment and support should be included in pediatric HIV management.