To investigate biomarkers of nutrition associated with chronic disease absence for an Aboriginal cohort.Screening for nutritional biomarkers was completed at baseline (1995). Evidence of chronic disease (diabetes, CVD, chronic kidney disease or hypertension) was sought from primary health-care clinics, hospitals and death records over 10 years of follow-up. Principal components analysis was used to group baseline nutritional biomarkers and logistic regression modelling used to investigate associations between the principal components and chronic disease absence.Three Central Australian Aboriginal communities.Aboriginal people (n 444, 286 of whom were without chronic disease at baseline) aged 15-82 years.Principal components analysis grouped twelve nutritional biomarkers into four components: 'lipids'; 'adiposity'; 'dietary quality'; and 'habitus with inverse quality diet'. For the 286 individuals free of chronic disease at baseline, lower adiposity, lower lipids and better dietary quality components were each associated with the absence at follow-up of most chronic diseases examined, with the exception of chronic kidney disease. Low 'adiposity' component was associated with absence of diabetes, hypertension and CVD at follow-up. Low 'lipid' component was associated with absence of hypertension and CVD, and high 'dietary quality' component was associated with absence of CVD at follow-up.Lowering or maintenance of the factors related to 'adiposity' and 'lipids' to healthy thresholds and increasing access to a healthy diet appear useful targets for chronic disease prevention for Aboriginal people in Central Australia.