Fothergill writes to an English physician, J. Woodforde, from Bath and Bristol in England and from Philadelphia. The letters concern their common interests in medicine, with comments on current events, American and Philadelphia society, and medicine in the United States.

The collection consists of diaries, 1890-1938, containing brief records of professional work and family events (49 vols.); also autobiography entitled "Memories for my boys," 1930 (B D713m), referring to his childhood and to his professional career and mentioning Franz Boas, William Comstock, Livingston Farrand, William W. Keen, S. Weir Mitchell, Elihu Root, and W. T. Sedgewick and also APS, University of Chicago, Johns Hopkins University, Yale University, and Wistar Institute (1 vol.); also a few miscellaneous papers, 1869-1932, chiefly letters to and from members of his family, and also Poultney Bigelow, Simon Henry Gage, and W. B. Van Ingen; two essays ("The Days of Man" and "A Venetian Night"): genealogical data; verses dedicated to his wife; extracts of letters to supplement his diaries.

This collection contains correspondence, reports, notes, and notebooks. Clarke's participation in various organizations is documented, including the American Philosophical Society, American Chemical Society, American Otological Society, and the American Society of Biological Chemists. His chemistry research is detailed in thirteen notebooks, 1903-1971 (the 1903 volume is on photographic chemistry and processes). There is also one volume on the clarinet, for Clarke was an expert clarinetist. The personal and family correspondence is principally with Mrs. Dorothy Clarke Middleton and Mrs. Agnes Helfreich Clarke.