This cross-sectional study investigated the relationship between individual-level markers of disadvantage, renal function and cardio-metabolic risk within an Indigenous population characterised by a heavy burden of chronic kidney disease and disadvantage.Using data from 20 Indigenous communities across Australia, an aggregate socio-economic status (SES) score was created from individual-level socio-economic variables reported by participants. Logistic regression was used to assess the association of individual-level socio-economic variables and the SES score with kidney function (an estimated glomerular function rate (eGFR) cut-point of <60 ml/min/1.73 m(2)) as well as clinical indicators of cardio-metabolic risk.The combination of lower education and unemployment was associated with poorer kidney function and higher cardio-metabolic risk factors. Regression models adjusted for age and gender showed that an eGFR < 60 ml/min/1.73 m(2) was associated with a low socio-economic score (lowest vs. highest 3.24 [95% CI 1.43-6.97]), remote living (remote vs. highly to moderately accessible 3.24 [95% CI 1.28-8.23]), renting (renting vs. owning/being purchased 5.76[95% CI 1.91-17.33]), unemployment (unemployed vs employed 2.85 [95% CI 1.31-6.19]) and receiving welfare (welfare vs. salary 2.49 [95% CI 1.42-4.37]). A higher aggregate socio-economic score was inversely associated with an eGFR < 60 ml/min/1.73 m(2) (0.75 [95% CI 063-0.89]).This study extends upon our understanding of associations between area-level markers of disadvantage and burden of end stage kidney disease amongst Indigenous populations to a detailed analysis of a range of well-characterised individual-level factors such as overall low socio-economic status, remote living, renting, unemployment and welfare. With the increasing burden of end-stage kidney disease amongst Indigenous people, the underlying socio-economic conditions and social and cultural determinants of health need to be understood at an individual as well as community-level, to develop, implement, target and sustain interventions.