An evaluation of molecular typing methods that can be applied to the food-borne pathogens Salmonella, Campylobacter, Shiga toxin-producing Escherichia coli and Listeria monocytogenes is presented. This evaluation is divided in two parts. Firstly, commonly used molecular typing methods are assessed against a set of predefined criteria relating to discriminatory capacity, reproducibility, repeatability and current or potential suitability for international harmonisation. Secondly, the methods are evaluated for their appropriateness for use in different public health-related applications. These applications include outbreak detection and investigation, attribution modelling, the potential for early identification of food-borne strains with epidemic potential and the integration of the resulting data in risk assessment. The results of these evaluations provide updated insights into the use and potential for use of molecular characterisation methods, including whole genome sequencing technologies, in microbial food safety. Recommendations are also made in order to encourage a holistic and structured approach to the use of molecular characterisation methods for food-borne pathogens; in particular, on the importance of structured co-ordination at international level to help overcome current limitations in harmonisation of data analysis and interpretation.