Background: Smoking prevention programs have been taught in schools to reduce the high smoking prevalence and its related problems among adolescent populations. Although short-term benefits have been observed, the long-term effectiveness of such programs appear to be inconsistent. This study aims at investigating the long-term impact of both health and Islamic focused interventions amongst students in Indonesia. Methods: At 6 months after completion of the interventions, 427 of the original 447 participants (control group=128, intervention groups=299) from a school-based cluster randomized control trial were re-assessed for their smoking knowledge, attitudes, intentions and behaviours using a self-report questionnaire. Data was analyzed according to the study's 2 × 2 factorial design with adjustment for baseline scores, school and classroom clustering effects and multiple comparisons. Results: Compared to the control group, significant long term effects were found for the health-based intervention program in improved health (β=4.3±0.4, p<0.001), Islamic (β=1.1±0.4, p=0.01) knowledge and a reduction of smoking attitudes (β=-11.5±1.8, p<0.001). For the Islamic-based intervention programs there was an improvement of health (β=3.7±0.4, p<0.001) and Islamic (β=2.2±0.5, p<0.001) knowledge and a reduction towards smoking attitude (β=-6.0±1.9, p<0.01) and smoking behaviors in the past month (OR=0.1, 95 % CI=0.0-0.8, p=0.03). The effects were greater but less than additive in the combined group for health (β=-3.2±0.9, p<0.001 for interaction) and Islamic knowledge (β=-2.3±0.9, p=0.01 for interaction) but were additive for smoking attitudes (β=6.1±3.2, p=0.07 for interaction). No significant effects on smoking intentions were observed at 6 months follow-up in the health or Islamic-based intervention programs. Conclusion: School-based programs can provide long term benefits on Indonesian adolescents' smoking knowledge and attitudes. Tailoring program intervention components with participants' religious background might maximise program effectiveness. A larger and more encompassing study is now required to confirm the effectiveness of this new Indonesia culturally-based program. Adolescents in similar areas might also benefit from this type of school-based smoking cessation program.