This article analyzes German debates on the microbiology of infectious diseases from 1865 to 1875 and asks how and when organic pollution in tissues became noteworthy for aetiology and pathogenesis. It was with Ernst Hallier's pleomorphistic microbiology that the organic character of alien material in tissues came to be regarded as important for pathology. The process that followed saw both vigorous biological critique and a number of medical applications of Hallier's work. Around 1874 contemporaries reached the conclusion that pleomorphous vegetation was most likely of little importance if not accidental in relation to the aetiology of infectious diseases whereas the idea of monomorphous micro-organisms facilitated a causal explanation. It was only then that notions such a pure cultures, bacterial specificity, etc. favored by Ferdinand Julius Cohn and his school became popular in medical circles.