Evaluation of the effectiveness of disinfection in pig farms is an integrál part of farm biosecurity management. Microbiological control of the disinfection efficiency provides information not only on compliance with the disinfection proceduře and the quality of sanitation, but also on the effectiveness of the ušed products and the concentration of disinfectant Solutions. Under the conditions of pig farms, the total number of microorganisms in three disinfectants containing different active substances (peroxides, iodophores and glutaraldehyde) in the samples after disinfection decreased by 3 log units of magnitude from 106 to 103 on 1 cm2 surface. This means, that in accordance with the Methodology of the SVA CR, the disinfection can be assessed as effective. The prerequisite for the effectiveness of disinfection is primarily compliance with the technological process of sanitation, taking into account the factors that may affect the effectiveness of disinfection, námely the level of microbial contamination of stables, including resistance of microorganisms, properties and use of disinfectants, etc.