Background Overweight and obesity lead to higher probability of individuals accessing primary care but adiposity estimates are rarely available at regional levels to inform health service planning. This paper analyses a large, community-derived clinical database of objectively measured body mass index (BMI) to explore relationships with area-level socioeconomic disadvantage for informing regional level planning activities. Materials and Methods The study included 91776 adults who had BMI objectively measured between 1 July 2009 and 30 June 2011 by a single pathology provider. Demographic data and BMI were extracted and matched to 2006 national census socioeconomic data using geocoding. Adjusted odds-ratios for overweight and obesity were calculated using sex-stratified logistic regression models with socioeconomic disadvantage of census collection district of residence as the independent variable. Results The prevalence of overweight or obesity was 79.2% (males) and 65.8% (females); increased with age to 74 years; and was higher in rural (74%) versus urban areas (71.4%) (p<0.001). Increasing socioeconomic disadvantage was associated with increasing prevalence of overweight (p<0.0001), obesity (p<0.0001) and overweight or obesity (p<0.0001) in women and obesity (p<0.0001) in men. Socioeconomic disadvantage was unrelated to overweight (p = 0.2024) and overweight or obesity (p = 0.4896) in males. Conclusion It is feasible to link routinely-collected clinical data, representative of a discrete population, with geographic distribution of disadvantage, and to obtain meaningful area-level information useful for targeting interventions to improve population health. Our results demonstrate novel area-level socioeconomic gradients in overweight and obesity relevant to regional health service planning.