Achieving optimal adherence to ARV’s in a rural paediatric population is challenging. Monitoring adherence by frequent viral load assay is not always feasible or sustainable in rural communities. A relatively cheaper, reliable, valid and sustainable measure of adherence for children is required for routine management. This study retrospectively assessed adherence outcomes using monthly pill count and viral load data, including reasons reported for non-adherence, in a paediatric cohort in rural KwaZulu-Natal, South Africa. Between 2008 and 2013, 78 children, mean age of 7.1 years, were enrolled in the CAPRISA 052 AIDS Treatment Programme. Monthly treatment adherence by pill count was categorized as either high (≥95%) or low (<95%). Overall median monthly adherence to treatment by pill count was 87.8% at month six, 88.9% at month 12 and 90.8% at month 24. However, the proportion of children with an undetectable viral load (< 400 copies/ml) was 84.0% (63/74), 86.6% (58/67), and 84.5% (49/58) at the three time points respectively. Agreement between pill count and viral load showed that only 33.9%, 36. 3% and 30.6% of children were truly adherent by pill count at months six, 12 and 24 respectively. In conclusion, this treatment programme demonstrated that adherence of >95% by pill count is not an ideal indicator of virological suppression in children aged six months – 13 years. Viral load assessment remains the gold standard for assessing treatment success in this age group.