Hoffmann is remembered for his research performed with zoologist Fritz Schaudinn (1871-1906) at the Charité Clinic in Berlin. In 1905 Schaudinn and Hoffmann discovered the bacterium that was responsible for syphilis, a spiral-shaped spirochete called Treponema pallidum. The organism was removed from a papula in the vulva of a patient with secondary syphilis. The two doctors documented their findings in a treatise called Vorläufiger Bericht über das Vorkommen von Spirochaeten in syphilitischen Krankheitsprodukten und bei Papillome.
Hoffmann left Germany during the era of National Socialism, but returned to Bonn after the war and established a laboratory. In the late 1940s he published two books about his life in medicine, titled "Wollen und Schaffen" and "Ringen um Vollendung".