One of the main problems confronting medicine in the 21st century is the increasing prevalence of bacteria that are resistant to antibiotics. This, combined with a shortage of new antibiotics under development, means that our ability to treat infectious diseases is rapidly diminishing. Because the over-use and misuse of antibiotics in many countries is likely to continue, new antibiotic-resistant bacterial strains will continue to emerge. In order to develop new means of limiting resistance development and the further transmission of antibiotic-resistant strains, it is essential that a concerted effort is made to gain a greater understanding of how the administration of particular antibiotics affects the antimicrobial susceptibility of potentially-pathogenic and commensal members of the indigenous microbiota of humans. The genetic basis of such resistance needs to be clarified together with the persistence and mode of transmission of antibiotic-resistant strains and the biological cost to the organism arising from its conversion to a resistant phenotype. It is also important to assess the ecological impact of antibiotic administration on the indigenous microbiota.