BackgroundThe bacterium Bacillus thuringiensis serovar israelensis (Bti) is used in many countries as a biological larvicide to control dipteran insects of the suborder Nematocera, especially mosquitoes and black flies. Bti is generally accepted to be target-specific and efficient, with low potential for development of resistance among the target species. However, even though Bti may have minimal direct effects on non-target organisms, it might potentially be associated with knock-on effects on food webs and other ecosystem properties, including biodiversity and ecosystem functioning. Evidence from previous research is mixed, with some finding no evidence for indirect effects on biodiversity and ecosystem-level properties, but others indicating that such effects are possible. The fact that many studies have been conducted by organisations coordinating the control programs, and that many of those studies have been published outside peer reviewed scientific journals, highlights the challenges for decision makers and others to assess the results of the existing studies. In this protocol we outline how we aim to systematically and transparently synthesise all available evidence in a forthcoming systematic review.MethodsWe will use six bibliographic databases/platforms and the online search engines Google and Google Scholar in searches for literature. Searches will also be made on specialist websites. We will screen the search results for eligibility in stage one based on title and abstract, and in stage two based on the full text of the material. At stage one, after testing and clarifying the eligibility criteria, two reviewers will split and single screen the search results. At stage two the articles will be screened independently by two reviewers. We have developed a preliminary critical appraisal tool that will be used as basis for assessing study validity. Each study will be critically appraised independently by two reviewers. Disagreements will be reconciled through discussions seeking to reach consensus. It is unclear whether a quantitative synthesis based on meta-analysis will be feasible. A narrative synthesis will include descriptive statistics outlining the evidence base in terms of bibliographic information and study metadata. A narrative synthesis table in the form of an Excel spreadsheet will be provided.