He entered the United States Army at the age of 17. When the Civil War broke out in 1861, he acted on the staff of General Thomas, being later appointed to the staff of General Howard in the Bureau of Emancipation of Slavery, at Washington DC. He went on to become the second librarian-in-chief of the Agricultural Department of the United States Government.
During his residence in Washington DC, and while still on the staff of General Howard, Eldridge entered the Faculty of Medicine at Georgetown University and graduated MD in 1868. There followed an appointment as Demonstrator of Anatomy. He later became a lecturer at his college and held this appointment until he left for Japan.
In August 1871 he arrived in Yokohama as Secretary and Physician to the Scientific Mission to Japan under General Horace Capron. The party consisted of General Horace Capron, T. Antisell (chemical engineer), A G Warfield (civil and land survey engineer) and Stuart Eldridge. They were honoured by the Emperor Meiji in Momiji Detatched Palace, Tokyo, with tea and the message "Through the cooperation of your work, I hope you will make the developement project in Hokkaido successful". Their arrival had occurred soon after the Meiji Restoration through which Japan opened her gates to the rest of the world after 300 years of isolation.
The Japanese Government appointed Dr Eldridge Surgeon-General of the Kaitakushi (Commissioner of Development Projects) and was stationed at Hakodate from May 1872. From this time he began to use "chf. Srg. Kaitakushi" after his name in his official letters to the Japanese Government. At Hakodate he established a medical school in Agust 1872, and trained Japanese students, both government sponsored and private. Among these was Kenkichi Rokkaku, the father of Masana and Takao Rokkaku who later took responsibility for the translation of Dr Eldridge's official letters that were discovered by Mr Yasuhisa Ohnishi, at the library of Sapporo College, Hokkaido in 1973 and 1976.Dr. Eldridge taught, according to one of his former students, Muraoka, almost entirely by himself on the following areas: anatomy, physiology, surgery, therapeutics, pharmacology, and obstetrics and gynaecology. Further, as extra-curricular lectures, he taught the study of the human body, literature, and required his students to observe while he treated patients. He also supervised his students' reading and insisted on their presence during medical examinations and surgical operations that he carried out himself. On occasions he made inspection trips to other hospitals in Hokkaido. In addition to these duties he published a magazine called "Kinsei-I-Setsu", measning "Modern Medical Science, said to be the first medical journal ever published in Japan in Japanese (beig translated by K. Honda, another of his medical students). Some 500 copies were distributed among medical students, practitioners and foreign residents in the employment of the Japanese Government, living in Tokyo, Yokohama and elsewhere. Upon the expiration of his contract with the Japanese Government, Eldridge would have wished to remain in Hokkaido and to continue teaching there. But the financial status of the Kaitakushi had become so poor that they could not afford it. Thus he settled in Yokohama where he remained in active work until his death. He held many offices, including that of the director of the General Hospital of Yokohama (later called the Bluff (Dutch) Hospital, Yokohama General Hospital etc.) in which appointment he was succeeded by Dr. Neil Gordon Munro, the well know British doctor-anthropologist on the Ainu. He was appointed a Member of the Central Sanitary Board by the Japanese Government in 1883, an Advisor to the Kanagawa Prefectural Sanitary Board. And in 1900 he was appointed the Vice-President of the Sei-I-Kwai - the Society for the Advancement of Medical Science in Japan. His services to the cause of the medical and sanitary progress in Japan were recognised by the Emperor Meiji, who conferred on him the Fourth Order of Merit wtih the Sacred Treasure in 1897, and the Third Order of Merit with the Sacred Treasure not long before his death.
He died on November 16th 1901 at the age of 58 in Yokohama. He was cremated and his ashes buried at the Yokohama Foreign Residents' Cemetery, which is still located on the bluff - a beautiful residential area of Yokohama overlooking the port.Among Eldridge's contributions to medical literature were papers on Beri-Beri, on the Arrow Poison of the Ainu, on Echinococci in the female bladder, on the Occurrence of Internal Aneurysm in European Residents in Japan (presented at the alumni meeting of the Bellevue Hospital during a return visit by Eldridge in 1894 and published in the New York Medical Journal in that year), on the Ubiquitous Microbe and on Plague.
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