Marked gender differences have been identified in cigarette smoking. In this study, we aimed to identify the gender-specific emotional and behavioral disorders among adolescent smokers and their consequent utilization of mental health services. We performed a nationwide survey study of an Israeli representative sample of 906 adolescents and their mothers. Mental disorders were assessed using the Development and Well-Being Assessment (DAWBA) Inventory. Levels of emotional and behavioral difficulties were evaluated using the Strengths and Difficulties Questionnaire (SDQ). Mental health services use and smoking habits were also assessed. Among non-smoker adolescents there were significant gender differences in almost all SDQ scales: emotional problems, pro-social, hyperactivity/inattention and conduct problems, whereas in the smoker group there was a difference only in the SDQ emotional problems scale (both self- and maternal-rated, P < 0.001 and P = 0.002, respectively). Only marginal difference was noted between males and females in help-seeking for emotional or behavioral problems. Over 50% of both male and female smokers in the study had untreated mental disorders (non-significant gender difference). The well-established gender differences in psychiatric symptomatology narrowed markedly in adolescent smokers; the typical gender difference in disruptive behaviors was lost in the adolescent smoking population. The implications of these findings are particularly relevant to developing more effective gender-specific programs to prevent youth smoking, to facilitate quitting and prepare primary care practitioners to identify mental disorders and behavioral problems in adolescents with a smoking history.