The American Board of Commissioners for Foreign Missions (ABCFM) was one of the largest Protestant missionary organizations active in Meiji Japan. The Japan Mission of the ABCFM gained a considerable following in the Kansai area, thus succeeding in establishing its sphere of influence there. The Japan Mission’s stronghold was the Doshisha School of Theology in Kyoto. The ABCFM missionaries in Kyoto also worked as teachers at other Doshisha schools. Doshisha eventually developed into one of the most prestigious private universities in Japan. Because of this particular background and setting, the present-day Doshisha University has become a major depository of historical papers relating to the Japan Mission. When I attended a research meeting at Doshisha several years ago, I was introduced to bundles of old, unsorted letters and documents that had long been left untouched in a storage cabinet. After only a glance I realized that in all probability they should be regarded as a constituent part of the Doshisha-owned Japan Mission papers. Nevertheless, no other scholars had ever bothered to examine their contents and details until I volunteered to do so. After a painfully time-consuming process of sorting and indexing, I have found that these materials numbering over 3,000 are tremendously informative sources on the history of the Japan Mission. Their most remarkable academic merit is that they include a variety of newly discovered manuscripts. Especially important among them are more than 2,000 pieces of correspondence from the ABCFM missionaries in Japan to Dewitt C. Jencks, who acted as the secretary of the Japan Mission from 1877 to 1887. Now that the indexing is nearly complete, I offer in this article an overview of these long neglected documents, and then demonstrate their historical significance.