The purpose of this study is to examine the preferences of Japanese consumers for certified forest products and estimate their price premiums using a discrete choice experiment. Although Japanese consumers have almost no opportunity to purchase forest certification products now, except paper and paper-related products, Japan may be a promising market with significant scope for increasing the demands for the forest certification products. Each choice task of our discrete choice experiment contained alternative wall renovation scenarios with interior wood materials showing five attributes. In 2008, 150 respondents living in Sapporo, northern Japan, completed our questionnaire, which contained a series of the choice tasks. To understand heterogeneous preferences and identify consumer segments in a systematic way, a latent class model was applied. The results show that the mean price premium on Forest Stewardship Council certification of interior materials was 40.5% under a ceteris paribus condition. However, two identified consumer segments both placed greater value on other attributes of the interior materials: dimensional stability and/or area of production. The results indicate that, for suppliers of forest products outside of Japan, the merit of forest certification and the demerit of foreign product will cancel each other out in Japan.