This study aimed to investigate gender differences in prevalence and correlates of depression and suicidal ideation among Korean adolescents. The analysis was performed using data from the 2009 Korean Youth Risk Behavior Web-based Survey. Logistic regression models and Wald chi-square statistics were used to identify the difference in the coefficients between the gender-specific models. Female students reported higher prevalence for depression(42.9%) than male students(31.4%), as well as higher level of suicidal ideation(girls:23.1%, boys:14.7%). Lower school achievement, worse self-rated health status, more conflicts were associated with higher level of depression and suicidal ideation. The impact of school achievement and conflicts with friends on mental health was greater among girls than boys. We suggest that the efficient strategies focusing on the gender differences should be established to improve mental health among Korean adolescents.