Microorganisms on surfaces of fruits and vegetables come not only from the natural environment but also from every stage of the food chain through which they have to pass (handling, packaging, and transportation). In the industrial processing plants, washing and disinfecting raw materials intended for direct consumption or production of unpasteurized juices is usually the only step in reducing the number of contaminating and pathogenic microorganisms. Particular attention should be paid to root vegetables because their edible parts have direct contact with the soil that is a habitat for many different groups of microorganisms. In the fruit and vegetable industry, sodium hypochlorite is the most commonly used disinfectant, which, despite its high efficiency, has many disadvantages: it causes corrosion of devices, may adversely affect the appearance, taste and smell of vegetables, and it contributes to the formation of dangerous trihalomethanes. In the paper, there are presented alternative to sodium hypochlorite substances used to disinfect root vegetables, mainly carrots, since those root vegetables are an important raw material in the Polish juice industry. The paper contains also a review of the literature relating to such compounds as acidified sodium chlorite, chlorine dioxide, hydrogen peroxide, peracetic acid, electrolyzed water, and ozone. There were depicted antimicrobial properties of disinfectants against yeasts, moulds, Gramnegative and Gram-positive bacteria as well as their disadvantages, advantages, mechanism of action, and effect on the organoleptic characteristics and lifespan prolongation of vegetables. Among the disinfectant described, the electrolyzed water and acidified sodium chlorite are highlighted owing to their high efficacy and no negative impacts on vegetable tissues, environment, and consumer health.