The safety evaluation of veterinary drugs intended for use in food producing animals relies heavily on the results of toxicity studies in laboratory animals, supported where possible by any data resulting from human exposure. The general approach involves the calculation of an acceptable daily intake which in turn can be used to elaborate maximum residue limits. It is an approach used in the European Union, in other countries and at the international level. In recent years, concern has been expressed over the presence of microbiologically active residues of veterinary drugs in food and their possible effects on the human gastrointestinal microflora. Methodologies for conducting microbiological safety studies have been investigated and approaches to microbiological safety assessments have been debated. The whole approach has proved to be controversial, partly because there are considerable doubts over the ability of low concentrations of antibiotic substances to produce adverse effects on the human gut flora and partly because there are no validated methods for testing for these attributes. This paper reviews the problems in some detail and discusses the regulatory consequences.