Dairy products, especially cheeses have a great nutritional value and a high consumption level around the world. Cheese is one of the most common foods over the world, and according to the International Dairy Foods Association report, cheese is the major manufactured dairy product, with the developing importance of the dairy industry. Considering a widespread consumption of cheeses, there is a growing concern regarding safety and microbiological quality. Bacterial and fungal growth on cheese represents both a quality and a food safety problem, and poses significant economic losses. Several microbial bacterial genera may destroy cheese; however, normally just some species of the family Enterobacteriaceae and some Gram positive bacteria dominate on specific types of cheese. Escherichia coli, Salmonella spp., Listeria monocytogenes and coagulase positive Staphylococci are the main contaminants. Cheese-contamination by bacterial species is dangerous due to toxin production, and some of the toxins have been shown to be stable under normal processing conditions. The main contamination source is the environment in the production facilities. Visible growth on cheese in the plant should be avoided in order to prevent problem of bacteria due to their growth and spreading. Identification of the contamination sources at or below species level is necessary and good hygiene practices could help reduce the microbial load to harmless level.