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Walter Pagel was born in Berlin, the youngest son of Julius Pagel, the Professor of Medical History at the Friedrich Wilhelms Universität, Berlin, where Pagel studied medicine. Pagel then worked at the Preussisches Institut für Infektionskrankheiten 'Robert Koch', Berlin, undertaking research in microbiology and immunology. In 1924 he moved to the Berlin Municipal Tuberculosis Hospital at Sommerfeld, where he pursued the immunological aspects of TB, working on theories recently advanced by Ranke. He continued to work as a pathologist in Germany until Hitler's accession to power in 1933, when he was dismissed from his post as a Jew. He then worked briefly in Paris before settling in England where he worked in Cambridge and London until his retirement in 1967. Between 1924 and 1967 Pagel was the author of around 120 publications on tuberculosis, including seven major monographs - of which Pulmonary Tuberculosis, 1939, was the OUP's standard textbook on the subject.
However, it was as a medical historian that Pagel was best known, concerned with the study of philosophy and religion in the 16th and 17th centuries, and primarily with the work of van Helmont, Paracelsus and Harvey. Pagel's first major historical monograph on van Helmont was published in 1930, but the majority of his historical research was carried out after his retirement from pathology work in 1967.