Purpose: This study was done to compare health risk behavior prevalence for youth living in metropolitan, medium sized and small cities or rural area, in order to enhance understanding regional differences. Methods: For this study, data from the 2006 Youth Health Risk Behavior Online Survey collected by the Korean Center for Disease Control were analyzed using SPSS. Results: In the metropolitan areas, prevalence for disease and perceived obesity were higher than in other areas. Lack of intense or moderate physical activity, obesity, fast food intake, and insufficient sleep showed higher prevalence than in rural areas. Prevalence of lifetime smoking, lifetime alcohol consumption, present alcohol use, fruit intake less than once a day, and not wearing a seat belt were higher in rural areas than in urban areas. Gender, smoking, and alcohol use were correlated. Spearman correlation between living with parent and skipping breakfast were significant. Smoking, alcohol use, and sexual behavior were correlated. Conclusion: As significant differences in prevalence of youth health risk behaviors exist between regional areas, health education and health promotion programs considering these differences have to be developed and implemented for adolescents. Programs for prevention of smoking and alcohol use, programs for improvement of fruit intake and safety are suggested for adolescents in rural areas, whereas programs to enhance physical activity and obesity management are suggested for adolescents in metropolitan areas.