The aim of this study is to examine the association between obesity, metabolic syndrome, physical activity, and elevated gamma-glutamyltransferase (GGT) among Indigenous Australian adults who did not drink alcohol. A cross-sectional study of 791 Indigenous adults in rural North Queensland communities was conducted between 1999 and 2001. Measures included serum GGT, fasting glucose, cholesterol, and triglycerides; resting blood pressure, BMI, and waist circumference; and self-reported physical activity, alcohol intake, and tobacco smoking. Central obesity measured by waist circumference in this population was significantly associated with elevated GGT independently of lifestyle behaviors (Adjusted odds ratio (OR) = 2.7, 95% confidence interval (CI): 1.2-6.0). Metabolic syndrome (International Diabetes Federation definition) was also strongly associated with increased GGT (OR = 2.6, 95% CI: 1.5-4.6). Habitual physical activity may be slightly protective (OR = 0.9, 95% CI: 0.5-1.6) in this group, but this was not clearly demonstrated in this study. Prevention of type 2 diabetes and cardiovascular disease in this population should emphasize "waist loss" and metabolic health through dietary and other interventions.