This work reviews the different analytical strategies based on capillary electromigration techniques developed for detecting microbial contaminants and their products in food matrices. Namely, this work presents an exhaustive and critical review, including works published till March 2007, on CE methods developed to detect and identify contaminants of microbial origin that represent a hazard to humans in foods. First, an overview on the strategies adopted for the analysis of intact microorganisms is presented. Next, CE methodologies based on the analysis of microbial constituents, including those based on genomics and proteomics approaches, are described. Finally, CE methods developed for detecting microbial toxins are discussed.