Objective The objective of this study was to determine the relationship between added sugar and dietary diversity, micronutrient intakes and anthropometric status in a nationally representative study of children, 1-8.9 years of age in South Africa. METHODS: Secondary analysis of a national survey of children (weighted n = 2,200; non weighted n = 2818) was undertaken. Validated 24-hour recalls of children were collected from mothers/caregivers and stratified into quartiles of percentage energy from added sugar (% EAS). A dietary diversity score (DDS) using 9 food groups, a food variety score (FVS) of individual food items, and a mean adequacy ratio (MAR) based on 11 micronutrients were calculated. The prevalence of stunting and overweight/obesity was also determined. RESULTS: Added sugar intake varied from 7.5-10.3% of energy intake for rural and urban areas, respectively. Mean added sugar intake ranged from 1.0% of energy intake in Quartile 1 (1-3 years) (Q1) to 19.3% in Q4 (4-8 years). Main sources of added sugar were white sugar (60.1%), cool drinks (squash type) (10.4%) and carbonated cool drinks (6.0%). Added sugar intake, correlated positively with most micronutrient intakes, DDS, FVS, and MAR. Significant negative partial correlations, adjusted for energy intake, were found between added sugar intake and intakes of protein, fibre, thiamin, pantothenic acid, biotin, vitamin E, calcium (1-3 years), phosphorus, iron (4-8 years), magnesium and zinc. The prevalence of overweight/obesity was higher in children aged 4-8 years in Q4 of %EAS than in other quartiles [mean (95%CI) % prevalence overweight 23.0 (16.2-29.8)% in Q4 compared to 13.0 (8.7-17.3)% in Q1, p = 0.0063]. CONCLUSION: Although DDS, FVS, MAR and micronutrient intakes were positively correlated with added sugar intakes, overall negative associations between micronutrients and added sugar intakes, adjusted for dietary energy, indicate micronutrient dilution. Overweight/obesity was increased with higher added sugar intakes in the 4-8 year old children.