Pepper described bone-marrow changes of pernicious anemia, though his actual description more closely resembles leukaemia.

"The most comprehensive 19th century American work on medicine.  Pepper assembled virtually all of the leading American physicians of the day, including D. Hayes Agnew, Roberts Bartholow, John Shaw Billings, William Byford, Alonzo Clark, J. Solis Cohen, Jacob Mendez DaCosta, Nathan Smith Davis, Louis Duhrling, Louis Elsberg, George Engelmann, Reginald Fitz, Austin Flint, Frank Foster, Samuel W. Gross, Allan McLane Hamilton, Abraham Jacobi, Mary Putnam Jacobi, Joseph Leidy, Alfred L. Loomis, William T. Lusk, Charles K. Mills, Francis Minot, S. Weir Mitchell, William Osler, William Pepper, James J. Putnam, Edward Seguin, Alexander Skene, Alfred Stille, T. Gaillard Thomas, James Tyson, William H. Welch, J. William White, James C. Wilson, and Horatio Wood, among others. This massive work provides remarkable insight into the practice of medicine when Osler was transitioning from a pathologist and part-time internist into a specialist in internal medicine. In Osler's memorial address that summarized Pepper's many achievements, he wrote of this system, "There had never been published in this country a composite work by native writers, corresponding to the System of Medicine by Reynolds or to Ziemssen's Encyclopedia. A circular was issued in November, 1881, to the joint authors, but it was more than three years before the first volume of the system was issued; the five volumes were then published in rapid succession, the fifth appearing in 1886. While unequal, as all such systems must necessarily be, it remains a great work, and contains articles which have become classical in American literature." (W. Bruce Fye).

Pepper’s type of adrenal medullary tumor.