A microflora of the ‘oscypek’ cheeses made of ewe’s, cow’s and mixed ewe’s and cow’s milk in 6 different locations (shepherd’s huts) in Southern Poland was investigated. A total bacterial count, a lactic acid bacteria count, coliforms, and yeast and moulds counts were determined in the fresh raw and smoked cheeses, as well as in cheeses stored for a period of 60 days in vacuum packages or in rice-grains at a temperature of 13°C and with a relative humidity of 90%. In the fresh smoked cheeses, it was checked whether or not Salmonella, Listeria, Staphylococcus aureus, and its toxins were present. In the ‘oscypek’ cheeses, lactic acid bacteria were the dominant microorganisms. The fresh smoked cheeses contained fewer microorganisms than the fresh ones examined directly after having been manufactured. There were significant differences both in counts and the composition of microflora in cheeses depending on their manufacturer and on the type of milk used to produce them. In fresh smoked cheeses, neither Listeria nor Salmonella were detected, and the coliform count was lower than the limiting standards as required for this species of microorganisms, whereas the Staphylococcus aureus count was slightly higher than the maximum allowable bacterial concentration. However, the results of an additional examination of cheeses according to 92/46 ECC did not show any occurrence of Staphyloccous toxins. The Total Bacterial Count decreased after the storage, and the coliforms presence was no longer detectable.