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At present microbiological risk are still the most frequent in the food industry and the disinfection is one of the procedures that can be carried out in the general prevention of foodborne infectious diseases. In the industrial process of food transformation the cleaning and disinfection procedures of surfaces and machinery have to be considered an integrate system with food production, a technological aspect that surely affects the finished product quality and safety. First of all to carry out properly these operations it is necessary that the factory and the equipment have been designed and constructed with high standard of hygiene to reduce the risk of contamination and to facilitate the sanitation. The procedures involve several stages which generally include pre-washing with water, cleaning, real disinfection, and a final rinsing with water. In order to assure a right disinfections of surfaces areas and of processing equipment the choice of disinfectant takes on particular importance. Some of the most widely used disinfectants include the hypochlorous acid, the chlorine dioxide and the peroxides like peracetic acid; the latter is widely used in soft drink and mineral water industries. The efficiency of these chemical agents depends on various factors as pH, temperature and the presence of organic substances with which the disinfectants can react to give by-products which can reduce the activity and can present toxicity. The use of hypochlorite may led to the formation of carcinogenic substance such as trialomethanes (THM) while the use of chlorine dioxide may lead to the formation of chlorites and chiorates. The peracetic acid is a good alternative compounds and it doesn't lead to the formation of carcinogenic by-products. In our researches we evaluated the effectiveness of peracetic acid to inactivate some resistant micro-organism like hepatitis A virus; our results show that in practical application in CIP (cleaning in place) it's necessary to use concentration of 600～ 1300mg/L of peracetic acid for 15～30min of contact time for an inactivation ＞ 99.99%.