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This study utilised a structural equation model to examine the relationship between diet quality, socioeconomic status, and cardiovascular disease (CVD) risk in South African learners. Confirmatory factor analysis was used to test the indirect effects model for diet, socioeconomic status, diet quality and cardiovascular risk using pre-existing cross-sectional data. The structural equation model was fit using Lavaan version 0.6–5 in R version 3.6.1. Data were analysed from 178 children and adolescents, aged 6–18 years, from five rural schools in Cofimvaba, South Africa. Latent variables were created for dietary quality, dyslipidaemia and the socioeconomic status of participants. A negative association was observed between socioeconomic status and dyslipidaemia in school-aged children (p = 0.029).