Background The effect of novel tobacco products, such as electronic cigarettes (EC) and heated tobacco products (HTP), on allergic rhinitis (AR) and asthma is not well known. Objective To evaluate the health effect of novel tobacco products on asthma and AR. Methods This study was conducted using large survey data on Korean middle and high school students. The relationship between current asthma/AR and novel tobacco products user status was evaluated. In order to compare the combined effects of conventional cigarette (CC), EC, and HTP use on current allergic diseases, the participants were classified into 18 groups based on CC (current, former, and never), EC (current, former, and never), and HTP (ever and never) status. Results A total of 60,040 participants representing 2,850,118 Korean adolescents were analyzed. Of all participants, 6.7%, 2.7%, and 2.9% were current CC, current EC, and ever HTP users, respectively. Current CC and ever HTP use was significantly associated with current asthma and AR in adjusted models. Current EC showed association with current AR but the association with asthma disappeared in the adjusted model. Among 18 groups, the groups including current CC use showed higher risk of current AR and asthma than never HTP‐never EC‐never CC group. The odds ratio of current asthma especially increased more in those who used EC and/or HTP with CC concurrently than those in the never HTP‐never EC‐current CC user group. Conclusion Using EC and/or HTP in adolescents might enhance the adverse effect of CC on AR and asthma. Among Korean adolescents aged from 12 to 18 years old, 6.7% and 2.7% currently use conventional cigarettes and electronic cigarettes, respectively and 2.9% ever used heated tobacco products. The use of conventional cigarette, electronic cigarette, and heated tobacco product, respectively and in combination increases the risk of allergic rhinitis and asthma in Korean adolescents. The use of heated tobacco product especially enhances the impact of conventional cigarettes on allergic rhinitis and asthma.