Molecular epidemiology allows us to trace specific microorganisms and mobile genetic elements and to assess their epidemiological and evolutionary relationships. Examples of molecular epidemiology investigations in veterinary hospitals are discussed. They demonstrate the great similarities with the situation in human medicine and the potential usefulness of molecular epidemiology in our fight against antimicrobial resistance and nosocomial infections in veterinary hospitals. A broad knowledge of the diversity of antimicrobial resistance determinants in some major groups of pathogens and commensals from animals such as Enterobacteriaceae, Pasteurellaceae, enterococci and staphylococci is emerging. However, there are important gaps in this knowledge, which are discussed here. Many more molecular epidemiology studies will be necessary to understand and follow the evolution of the problem in veterinary medicine and agriculture on a global scale. To be able to build useful surveillance programs and reliable epidemiological models, and to identify critical intervention points, we need to improve our understanding of antimicrobial resistance at the animal and farm levels. Studies assessing the dynamics of bacterial populations and of resistance determinants at these levels are desperately needed. Understanding the relationships between antimicrobial resistance, colonization factors, and virulence also represents a major issue for which molecular epidemiology investigations will be needed.