Background: Health intervention for adolescents is very crucial as the investment in building healthy life style and quality of learning process. Studies on health risk issues on adolescents in school setting and its relationship to academic score is limited. This study aims to describe behaviour risk factors among adolescents aged 12 to 15 years, and in particular studying smoking behaviour among male students. Method: This is a cross sectional study in the school setting. Samples are adolescents aged 12 to 15 years. This cross sectional study used pre-constructed self administered questionnaire adapted from Global School-based Health Survey (GSHS) WHO and was conducted during July-August 2006. Total sample in this study was 1,651 students of 29 junior high schools in Depok, West Java, Indonesia. Descriptive data analysis was used to describe the proportion distribution of health risk issues and smoking behaviour. Results: The major behaviour health risk issues includes smoking, diet related risk behavior, unhygienic behavior, injury, physical activity and mental health related behaviour. The proportions were significantly different between male and female. The proportion of smoking 39.2% among males and 3.7% among females. In comparison with the male students who never smoked, those who smoke had significantly lower mean of academic score (mean: 6.90 (95%CI: 6.79-7.01) vs 7.13 (95% CI: 7.06-7.20) p-value: 0.001) and higher school absenteeism (6.4 vs 3.5, p-value: 0.001). Conclusion: Males and females adolescents had significantly different health risk issues. Involuntary smoking shows the highest proportion of health risk behaviour among both male and female adolescents. Smoking behaviour has significant relationship with the academic score among male adolescents.