Objective: This study aimed to identify dyslipidaemia in human immunodeficiency virus (HIV)-infected children. This was part of a larger study aiming at the treatment of dyslipidaemia in this population. Design: A cross-sectional quantitative study design was used. Setting: The Paediatric Outpatient Department HIV Clinic at Dr George Mukhari Academic Hospital (Garankuwa, Pretoria). Subjects: Children who received antiretroviral treatment (ART) for at least six months and were virologically supressed. Outcome measures: Fasting lipograms were evaluated against American paediatric thresholds for dyslipidaemia (NCEP ATPIII guidelines), and z-scores for weight-for-age (WAZ) and height-for-age (HAZ) were interpreted. Results: In total, 140 children were enrolled, median age at enrolment was 64.5 months (interquartile range IQR 42.5–94.6) and 51% were female. Median period of ART use was 34.0 months (IQR 23.2–52.8). Median ART commencement age was 18 months (IQR 8.1–34.0). Lipid profile results were available in 108 of the 140 children. Total cholesterol was classified borderline in 33% and elevated in 11% of the children. LDL cholesterol was borderline in 24% and elevated in 7%. HDL cholesterol was borderline in 20% and low in 30%. Triglyceride levels were borderline in 29% and elevated in 39% of the children. Children were considered as having dyslipidaemia if one or more of the four lipid profile levels were abnormal, or if at least two were borderline. By these criteria, 75% of the group were dyslipidaemic. A significant negative correlation was found between dyslipidaemia and enrolment HAZ indicating stunting (r-value −0.31; p < 0.05), also between dyslipidaemia and months’ duration on ART (r-value −0.25; p < 0.05) and a significant positive correlation was found between initiation on protease inhibitor (PI)-based regimen and dyslipidemia (p < 0.05). Conclusion: The prevalence of dyslipidaemia in HIV-infected children receiving ART is high. Participants who were stunted, or had a shorter ART duration, and those initiated on a PI-based regimen were more likely to have dyslipidaemia.