Cheese can contain regulated disinfection by-products (DBPs), mainly through contact with brine solutions prepared in disinfected water or sanitisers used to clean all contact surfaces, such as processing equipment and tanks. This study has focused on the possible presence of up to 10 trihalomethanes (THMs) and 13 haloacetic acids (HAAs) in a wide range of European cheeses. The study shows that 2 THMs, (in particular trichloromethane) and 3 HAAs (in particular dichloroacetic acid) can be found at μg/kg levels in the 56 cheeses analysed. Of the two types of DBPs, HAAs were generally present at higher concentrations, due to their hydrophilic and non-volatile nature. Despite their different nature (THMs are lipophilic), both of them have an affinity for fatty cheeses, increasing their concentrations as the percentage of water decreased because the DBPs were concentrated in the aqueous phase of the cheeses.