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Background: We examined the body mass index (BMI) of students attending Seventh-day Adventist (Adventist) schools in Australia in 2001 and 2012. Methods: A total of 3069 students attending Adventist schools in Australia responded to a health and lifestyle survey in 2001 (N = 1335) and 2012 (N = 1734). The survey captured self-reported height and weight, demographics (age, sex, year level, religion), and select health behaviors. Results: Compared with national norms, lower rates of overweight and obesity were observed in the study cohort, but higher rates of underweight. There was no change in the mean BMI of the students attending Adventist schools in Australia from 2001 to 2012. Regression analyses indicated that a lower BMI was associated with age, sex, more regularly eating breakfast, consuming less soft drink, and having a regular exercise program. The students reported a high consumption of fruits, vegetables, and whole grains compared with Australian national norms, and 29% claimed to be vegetarian. Conclusions: Students attending Adventist schools appear to have a lower prevalence of overweight and obesity than the secular population, but a higher prevalence of underweight. The mechanisms through which Adventist schools may influence student's BMI warrants further investigation.