Abstract Background Bullying in schools has been associated with suicidal ideation but the confounding effect of psychiatric morbidity has not always been taken into account. Our main aim was to test the association between bullying behavior and early stages of suicidal ideation in a sample of Greek adolescents and to examine whether this is independent of the presence of psychiatric morbidity, including sub-threshold symptoms. Methods 5614 pupils 16-18 years old and attending 25 senior high schools were screened in the first phase and a stratified random sample of 2431 were selected for a detailed interview at the second phase. Psychiatric morbidity and suicidal ideation were assessed with the revised Clinical Interview Schedule (CIS-R) while bullying was assessed with the revised Olweus bully/victim questionnaire. Results Victims of bullying behavior were more likely to express suicidal ideation. This association was particularly strong for those who were bullied on a weekly basis and it was independent of the presence of psychiatric morbidity (Odds Ratio: 7.78; 95% Confidence Interval: 3.05 - 19.90). In contrast, being a perpetrator ("bullying others") was not associated with this type of ideation after adjustment. These findings were similar in both boys and girls, although the population impact of victimization in the prevalence of suicidal ideation was potentially higher for boys. Conclusions The strong cross-sectional association between frequent victimization and suicidal ideation in late adolescence offers an opportunity for identifying pupils in the school setting that are in a higher risk for exhibiting suicidal ideation.