BackgroundTo document albuminuria prevalence and its associated factors in Aboriginal and Torres Strait Islander (TSI) adults with high renal and metabolic risks from 19 rural and remote north Queensland communities.MethodsOne thousand nine hundred seventy-one indigenous adults were enrolled in 1998 and 566 completed follow up in 2007 in this population-based study. Measurements included weight, waist circumference (WC), blood pressure (BP), fasting glucose, lipids, gamma-glutamyltransferase (GGT), urinary albumin creatinine ratio (UACR), smoking, alcohol intake and physical activity (PA). Albuminuria was defined as an UACR > =2.5 g/mol in males and > =3.5 g/mol in females. The association between albuminuria and biomedical factors was assessed with generalised linear modelling.ResultsBaseline albuminuria prevalence was 19.7 % (95 % CI: 18.0–21.6 %). Follow up prevalence was 42.4 % (95 % CI: 38.4–46.5 %) among the 566 adults having the 2nd UACR measurements. Follow-up albuminuria was associated with fasting glucose of 5.4 mmol/L (OR 2.5, 95 % CI 1.5–4.2), GGT tertiles in a dose-response manner (OR 2.0 for 2nd and 3.7 for 3rd tertile, p for trend <0.001), and abdominal overweight and obesity (OR 2.1, 95 % CI 1.1–3.9 and 5.4, 95 % CI: 2.2–13.5 respectively). Aboriginal people with diabetes were three times more likely of having albuminuria compared to TSI counterparts, while TSI smokers had twice the likelihood (95 % CI 1.2–3.2). At both baseline and follow up, albuminuria was more prevalent among older participants.ConclusionsIndigenous Australians in north Queensland are at high risk of albuminuria. Overweight and obesity, glycaemia, increased GGT, and smoking were associated with albuminuria at baseline and/or follow up.Electronic supplementary materialThe online version of this article (doi:10.1186/s12882-015-0200-8) contains supplementary material, which is available to authorized users.