Background: Most studies of chronic disease in Aboriginal people have described prevalence on cross-sectional surveys. We estimated incidence rates through a longitudinal study, (mean 10.4 years follow up), in one high risk Northern Territory Aboriginal community. Methods: Community-wide surveys, each with >80% participation, were conducted from 1992–1996 and 2004–2006, and defined rates of albuminuria (ACR > 3.4 g/mol), hypertension (BP > 140/90) and diabetes (history, medicines or defining glycemia). Results: In the first survey of 962 adults (18+ years, median 32.6 years), 45.7% had albuminuria, 23.5% had hypertension and 13.5% had diabetes, while 39.3% had none of these conditions. In the second survey (n = 1153 adults, median age 34.2 years) these rates were 44.8%, 17.4% and 19.5%. Among 250 adults with no abnormality on the first screen who participated in the second screen, 54.7% had developed one or more problems: 45.1% had developed albuminuria, 16.2% had developed hypertension and 15.6% had developed diabetes. These minimum incidence rates of 4.3, 1.6 and 1.5 per person year translate to rates of 8.6, 3.2 and 3.2 per person year if the conditions appeared halfway through the follow-up period. The proportion of previously unaffected people who had developed any one of these conditions by the second screen was 54.7%, with an estimated incidence of 11% per year if those conditions appeared mid-way through the follow-up period. Discussion: Incidence rates of new disease are striking in this youthful Aboriginal population. Recent improvements in mortality and renal failure are clearly due to better surveillance and treatment, rather than fundamental diminution of risk. This information shows that those efforts cannot be relaxed. Specific targets for primary prevention remain obscure while the nature of accentuated susceptibility is not understood.