Objective: Some Japanese smokers imported Japanese cigarette brands from other Asian countries for personal use because of the increase in tobacco tax in 2010, which meant that privately importing the cigarettes was cheaper than purchasing them in Japan. We assumed that the health hazards of locally made cigarettes were different from those of privately imported cigarettes, despite the brands being the same. In this study, we carried out a comparative toxicological analysis of domestic and privately imported cigarettes. Methods: Privately imported cigarettes of five brands and domestic cigarettes of the brand named “MILD SEVEN ORIGINAL” were selected for the study. The level of polycyclic aromatic hydrocarbons (PAHs) in mainstream smoke was determined by high-performance liquid chromatography using fluorescence detection. The mutagenicity of mainstream smoke was assessed using the Salmonella typhimurium strains TA100, TA98, and YG1024 with the metabolic activation system (S9mix) by preincubation assay. The levels of heavy metals in cigarette fillers were determined by inductively coupled plasma-mass spectrometry. Results: The level of PAH in the mainstream smoke from the privately imported cigarettes was higher than that in the smoke from the domestic cigarettes. However, the mutagenic activity of the mainstream smoke from the privately imported cigarettes was equivalent to that from the domestic cigarettes. The levels of nickel and cadmium in the fillers of the privately imported cigarettes were higher than those in the domestic cigarettes. Conclusion: The levels of constituents in the fillers and mainstream smoke from the privately imported cigarettes were higher than those in the fillers and mainstream smoke from the domestic cigarettes. The majority of Japanese smokers are unaware of these findings. The guidelines regulating tobacco products recommend that articles 9 and 10 of the World Health Organization (WHO) Framework Convention on Tobacco Control should be fully implemented in Japan.