|South Africa faces a huge Human Immunodeficiency Virus (HIV) burden with more than 400,000 children currently on antiretroviral therapy (ART). Studies on lipid and haematological profile changes in paediatrics are of particular interest since these children are exposed to ART in the course of a developmentally significant period and will possibly have longer collective exposure to ART. As such, monitoring for adverse effects, including lipid and haematological abnormalities, is essential for curtailing morbidity and mortality rates of children on ART. There is a dearth of studies assessing lipid and haematological abnormalities in the South African paediatric population on ART where genetic differences, co-morbidities, malnutrition and use of traditional medicines, all influence the safety profile of a drug. The goal of this study was twofold: Firstly to identify a suitable parameter for assessing lipid and haematological abnormalities in paediatrics on Antiretroviral (ARV) treatment using available secondary data and secondly, to assess prescriber adherence to routine monitoring tests in the ART guidelines. This study was a retrospective review of secondary data obtained from 168 patient clinical records at a Community Health Centre in the Cape Metropole, Western Cape and corresponding laboratory data from the National Health Laboratory Service (NHLS) database. Appropriate cholesterol, triglyceride, haemoglobin and neutrophil test results were compared against the standard reference ranges/values. The Chi-Squared test identified associations between total cholesterol (TC) /triglycerides and haemoglobin (Hb)/neutrophil and other independent variables. Evaluation of health care provider adherence to routine monitoring tests was assessed against relevant national ARV management guidelines. There was a paucity of baseline data for all laboratory markers and infrequent follow-up tests were ordered by healthcare providers. This precluded the measurement of changing lipid and haematological levels and an alternative parameter, viz., the highest available laboratory test value for each marker per patient, was assessed against reference values/ranges. Only nine out of the 36 (25%) patients on an AZT regimen had any Hb or neutrophil laboratory tests performed and 23 and two out of 97 (24% and 2%) patients, respectively, on a protease inhibitor (PI) had a TC and triglyceride laboratory test performed. Anaemia was detected in 45.5 % of children below five years of age, in 21.7% between ages of six and 11 and in 65.5 % between 12 and 14 years of age. Neutropenia was detected in 25.6% of children below five years of age and in 50% aged between six and 11. Hypercholesterolemia was found in 13.1% of patients. The only statistically statistical associations were found between the TC and CD4 count in children aged six to 14 years (χ2=5.000; p=0.025) and between neutrophil counts and viral load in children aged six to 14 years (χ2=6.4532; p=0.0240). A significant association was also found between Hb levels and viral load (χ2=7.000; p=0.008). In the absence of baseline test results and routine monitoring of haematological and lipid profiles, this study presents a potential alternative marker for assessing lipid and haematological abnormalities using the highest level of neutrophil, Hb, TC and triglycerides recorded for each patient.