The level of evidence supporting different disinfection and cleaning procedures performed in healthcare settings worldwide is low. With respect to environmental surfaces, the final assessment of whether use of disinfectants rather than detergents alone reduces nosocomial infection rates in different clinical settings still awaits conclusive study. It must be kept in mind that the effect of surface disinfection is only transient microbial contamination will have reached its former level within a few hours. While resistance to biocides is generally not judged to be as critical as antibiotic resistance, scientific data support the need for proper use, i.e. avoidance of widespread application, especially in low concentrations and in consumer products. The decontamination ability of the substances used; prevention of resistance; and safety for patients, personnel and the environment; are the cornerstones that interact with each other. Future work should focus on this complex background. Targeted disinfection of environmental surfaces (those frequently touched) is an established component of infection control activities to prevent the spread of nosocomial (multi-resistant) pathogens, but of lesser importance than proper hand hygiene. However, since the use of disinfectants may pose a danger to staff, patients and the environment, prudent use combined with the application of proven safety precautions is important. Since emerging resistant pathogens will challenge healthcare facilities in future even more than today, well-designed studies addressing the role of disinfection in the healthcare-setting are needed.