Background Physical inactivity and obesity are major risk factors for type 2 diabetes (T2D). Aim To investigate whether if the association between obesity and diabetes is modified by levels of physical activity in the Chilean population. Material and Methods Cross-sectional study including 4,712 participants from the 2009-2010 National Health Survey. Diabetes was determined when participants referred having the disease or had a fasting glucose ≥ 126 mg/dl. Physical activity level was assessed using the Global Physical Activity Questionnaire. The association between diabetes, obesity and physical activity was determined using logistic regression analysis. Results Compare to active and normal weight subjects (reference group), the risk for T2D was higher in active individuals with overweight (Odds ratio (OR): 2.85 95% confidence intervals (CI): 1.76- 4.61 p < 0.01). The risk among inactive but normal weight participants (OR: 2.12 95% CI: 1.49- 3.01, p < 0.01) was of lower magnitude and was even higher among inactive and overweight individuals (OR: 3.22 95% CI: 2.10 – 4.93, p < 0.01). Similar results were found for obesity and central obesity. Conclusions Individuals who are physically inactive and have a high adiposity level have an increased risk for T2D compared to active individuals with normal BMI.