In 1999, the National Food Consumption Survey found serious risk of dietary deficiency for a number of micronutrients in 1- to 9-year-old children in South Africa. To address these shortfalls, fortification with vitamin A, thiamine, riboflavin, niacin, vitamin B6, folic acid, iron and zinc of maize meal and bread flour was made mandatory in 2003. The aim of this study was to examine micronutrient intakes of 1- to <10-year-old children after nearly 20 years of fortification in two of the most urbanized and economically active provinces, Gauteng (GTG) and the Western Cape (WC). A multistage stratified cluster random sampling design and methodology was used. Households were visited by fieldworkers who interviewed caregivers and obtained dietary intake data by means of a multiple-pass 24-h recall. Two additional 24-h recalls were completed among a nested sample of 146 participants to adjust the single 24-h recall data of the total sample using the National Cancer Institute Method. Results show that median intake of all the fortification nutrients were above the estimated average requirement (EAR), with the only concern being folate in the WC. Between a quarter and a third of children in the WC, where maize porridge intake was significantly lower than in GTG, had a folate intake below the EAR. Nutrients that are not included in the fortification mix that remain a serious concern are calcium and vitamin D, with intake of dairy and vitamin D sources being very limited in both provinces. The improvement in micronutrient intakes of children is encouraging, however the outstanding nutrient deficiency risks need attention.