This paper reconceptualizes Thomas Clifford Allbutt's contributions to the making of scientific medicine in late nineteenth-century England. Existing literature on Allbutt usually describes his achievements, such as his design of the pocket thermometer and his advocacy of the use of the ophthalmoscope in general medicine, as independent events; and his work on the development of comparative pathology is largely overlooked. In this paper I focus on this latter aspect. I examine Allbutt's books and addresses and claim that Allbutt argued for the centrality of comparative pathology in the advancement of medical knowledge. He held that diseases should be studied as biological phenomena and that medicine should be made a biological science. He also argued that comparative pathology should be based upon the idea of evolution, and its study should embrace other nineteenth-century sciences including neurology, embryology and bacteriology. Allbutt's writings reveal that his endorsement of comparative pathology (1880s to 1920s), his promotion of the use of the ophthalmoscope and the thermometer in clinical medicine (early 1870s), and his support of the hospital unit system (1910s to 1920s) were part of a single programme. All were grounded in his scientific vision of medicine which emphasized a research culture, a stringent nosological attitude and an integration of laboratory sciences and clinical medicine. (Contains 110 footnotes.)