Disinfection as a public health intervention enjoyed a resurgence in popularity from the 1870s, with national and local legislation empowering and encouraging local authorities to undertake disinfection of houses, items and people. The parallel trends of the development of germ theories and the increasing focus on preventative public health prompted the development of an integrated programme of disinfection, which, alongside notification and isolation, was directed against epidemic and endemic infectious diseases. Procedures such as sulphur fumigation, heat treatment and use of chemical liquids were used to purify infected places, people and objects. The underlying rationale was that the increasingly exacting standards of disinfection required in the new era of germ theory needed to be done by professional medical officers of health, rather than the “amateur” public, in order to protect the public health. Technological and chemical change, and new laboratory research, however, presented an increasingly wide range of disinfection methods; choosing the most effective method was a difficult task. Local medical officers of health were expected to negotiate this new and troubling landscape to ensure that their policies prevented disease outbreaks. This paper examines differing practices of local authority disinfection between 1870 and 1914, and the effect that changes in knowledge had over day-to-day action. In particular, I will highlight the ambivalent effect that germ theory had on local disinfection practice and the gap between laboratory based knowledge and evidence derived from practical experience. This gulf in the usefulness and use of knowledge meant that despite efforts to professionalise disinfection, local authority practice increasingly diverged from the ideal promulgated by central government and definition researchers. This tension lay at the heart of seemingly paradoxical changes in disinfection theory and practice in the second half of the nineteenth century, and illustrate the complexities of the impact of germ theory on public health policy.