Purpose: To examine whether traditional and cyber bullying victimization were associated with adolescent’s mental health problems and suicidal ideation at two-year follow-up. Gender differences were explored to determine whether bullying affects boys and girls differently. Methods: A two-year longitudinal study was conducted among first-year secondary school students (N = 3181). Traditional and cyber bullying victimization were assessed at baseline, whereas mental health status and suicidal ideation were assessed at baseline and follow-up by means of self-report questionnaires. Logistic regression analyses were conducted to assess associations between these variables while controlling for baseline problems. Additionally, we tested whether gender differences in mental health and suicidal ideation were present for the two types of bullying. Results: There was a significant interaction between gender and traditional bullying victimization and between gender and cyber bullying victimization on mental health problems. Among boys, traditional and cyber bullying victimization were not related to mental health problems after controlling for baseline mental health. Among girls, both traditional and cyber bullying victimization were associated with mental health problems after controlling for baseline mental health. No significant interaction between gender and traditional or cyber bullying victimization on suicidal ideation was found. Traditional bullying victimization was associated with suicidal ideation, whereas cyber bullying victimization was not associated with suicidal ideation after controlling for baseline suicidal ideation. Conclusions: Traditional bullying victimization is associated with an increased risk of suicidal ideation, whereas traditional, as well as cyber bullying victimization is associated with an increased risk of mental health problems among girls. These findings stress the importance of programs aimed at reducing bullying behavior, especially because early-onset mental health problems may pose a risk for the development of psychiatric disorders in adulthood.