BackgroundDiabetic individuals have a largely increased risk of lower extremity amputation (LEA) compared with non-diabetic patients. Prior systematic reviews of incidence of LEA have some limitations with respect to lack of consensus in the definition of LEA, level of LEA (all, major, minor), and definition of source population (general population or population with diabetes at risk). The purpose of our review is to evaluate the incidence of LEA in the diabetic population and its differences with regard to sex, ethnicity, age, and regions; to compare the incidence rate (IR) in the diabetic and non-diabetic population; and to investigate time trends.Methods/designWe will perform a systematic literature search in MEDLINE, Embase, Web of Knowledge, and publisher databases such as Journals@OVID and ScienceDirect. We will develop comprehensive systematic search strategies according to established guidelines for meta-analyses of observational studies in epidemiology (the MOOSE group). Two authors will independently screen abstracts and full text of all references on the basis of inclusion criteria with respect to types of study, types of population, and the main outcome. We will exclude studies if they report solely incidences of LEA among persons with diabetes mellitus when referring to the total population (diabetic and non-diabetic) and not exclusively to the diabetic population. Data extraction and assessment of risk of bias will be undertaken by two review authors working independently. We will assess incidence rate (IR) or cumulative incidence (CumI), relative risk of amputations comparing the diabetic to non-diabetic populations, cause of LEA, and type of diabetes. If we find subsets of studies to be homogeneous enough, we will perform meta-analyses for incidence rates by Poisson generalized linear mixed models (GLMM).Systematic review registrationPROSPERO CRD42015017809Electronic supplementary materialThe online version of this article (doi:10.1186/s13643-015-0064-9) contains supplementary material, which is available to authorized users.