Reviewing previous scientific research results of microbiological quality of raw milk and Paški, Krčki and Domiati cheese are shown. Paški and Krčki cheese are famous Croatian hard sheep cheese, while Domiati cheese, which ripens in brine, is very popular in Egypt and Middle East countries. In the production of most traditional cheeses raw milk is used, which can be source of pathogenic bacteria and spoilage microorganisms. Therefore, knowledge of the origin, the way of their growth in milk and their destruction is crucial to obtain a safe cheese. An effective method to control growth of microorganisms is the application of the HACCP system in the production plant and the application of the principles of good manufacturing, agricultural and veterinary practices in the primary production of milk. During the experimental period the average number of somatic cells in the sheep's milk used in the manufacture of Krčki cheese was 407 000 mL-1 and the total bacterial count of 750 500 cfu mL-1. The sheep's milk used in the manufacture of Paški cheese during the experimental period of three years average number of somatic cells was less than 200,000 mL-1 and the total bacterial count of less than 5000 cfu mL-1 (n =720). Based on the results of hygienic quality of milk both sheep milks comply criteria prescribed by Pravilnik (NN 102/00).The results of microbiological analysis on the incidence of pathogenic bacteria in the Paški cheese (n=240) during the three-year period were negative, and are fully compliant with the provisions of the Regulation for microbiological criteria for food (NN156/08). In contrast, 45% samples of Krčki cheese in the investigation period were positive for Staphylococcus. aureus and Escherichia coli bacteria. Microbiological analyzes of cow's milk (n=50) and Domiati cheese (n=50) was found the presence of pathogenic bacteria over the allowable limit prescribed by Regulation EC 853/2004 and EC 1008/2000. Compared with the Paški and Krčki cheese, Domiati cheese is more susceptible on the incidence of pathogenic bacteria. The reason for this is the high percentage of moisture and higher pH value in cheese curdand specificity of production technology, which uses low-temperature processing of cheese curd and short duration of ripening.