Antimicrobial agents are associated with side-effects, which are usually tolerated because the benefits of treatment outweigh the toxic effects. Clinicians know about these side-effects but are less likely to understand additional adverse events, such as the overgrowth of resistant microorganisms. Overgrowth can itself precipitate a secondary infection, which can be more difficult to treat. Resistant organisms then spread to other patients and the environment, and contribute to increasing antimicrobial resistance worldwide. Organisms exposed to antibiotics undergo molecular changes that might enhance virulence. Enhanced pathogenicity would affect patients, particularly if the organism is also multiply resistant. Clinicians have a responsibility to select the correct antibiotic as soon as they have diagnosed infection, but an absence of microbiological understanding and ignorance of the potential environmental effects have contributed to inappropriate prescribing. The less obvious results of antimicrobial consumption probably go unrecognised in routine clinical care.