Objective: To measure the nicotine and tobacco-specific nitrosamine (TSNA) contents in whole tobacco from a variety of Japanese domestic cigarette brands and to determine mutagencity. Methods: The test cigarettes were the top ten best selling cigarette brands in Japan in 2006. The nicotine content in whole tobacco was measured by a modified version of the CORESTA Recommended method. The level of TSNA was measured by a modified version of the Health Canada method. Mutagenicity was assessed using the Salmonella typhimurium strains TA100, TA98 and YG1024 with the metabolic activation system (S9mix) by preincubation assays. Results: The nicotine content in the test cigarettes averaged 15.7±1.2 mg/g, and was in the range between 13.7 and 17.2 mg/g. The level of TSNA averaged 1,750 ng/g, and was in the range between 931 and 2,490 ng/g. Mutagenicity was pseudopositive in several samples of the YG1024 tester strain with and without S9mix. Conclusion: The cigarettes brands were categorized into four groups (Ultra-low, Low, Medium, and High) based on the nominal nicotine yield figures printed on the cigarette packets. The nicotine content in whole tobacco of the High group was the highest. However, the level of TSNA of the high group was the lowest. The analyses of hazardous chemical compounds in whole tobacco can contribute to the reduction and regulation of the toxicity of tobacco products.