Objectives: The aim of this study was to measure secular trends in health risk behaviors among middle and high school students in Korea between 2005 and 2009 by using data from the Korea Youth Risk Behavior Web-based Survey(KYRBS). Methods: The analyses were performed using data from the 2005, 2006, 2007, 2008, and 2009 KYRBS, which included a nationally representative sample of middle and high school students. A total of 34 health behavior indices were used for the assessment of secular trends in health risk behaviors. Logistic regression models were used to identify statistically significant secular trends in health risk behaviors, after adjusting for gender and grade. Linear and higher-order time variables were simultaneously entered into the statistical models. Results: There was evidence of small, but statistically significant increasing or decreasing trends in certain health risk behaviors. Secular trends in health risk behaviors varied by gender. Conclusions: This study indicates that between 2005 and 2009, changes in health risk behaviors among Korean adolescents were generally small, but represented statistically significant increases or decreases. Further research should explore why certain health risk behaviors are increasing or decreasing and what types of interventions are most effective.