This report reviews recent studies on infectious complications and antibiotic prophylaxis in common urological instrumentation. As a result of variations in the definitions of infectious complications and inconsistencies in study design and risk factor analysis there is presently limited clear-cut evidence for giving definite standards regarding antibiotic prophylaxis for most urological interventions. The consequences are that patients may be exposed to unnecessary hazards and the healthcare system to additional costs. Nonetheless, most authors agree that patients should have sterile urine at urological instrumentation and that any other detected risk factor should be controlled. When antibiotic prophylaxis is considered, it should be timed properly before the intervention, which varies with the type of intervention and the choice of antibiotic, and should last for a limited period of time. In most common urological manipulations, correctly administered oral prophylaxis has been shown to be as effective as intravenous prophylaxis. A series of guidelines aimed at keeping the rates of healthcare-associated infections and the level of bacterial resistance as low as possible should, in combination with the rational use of antibiotics, be one of several marks of quality of a urological centre. To achieve this goal, new well-designed studies considering different regimens, risk factor analysis and economical analysis should be encouraged.