To solve the problem of raw milk surplus, the Korean government encouraged the farmstead milk processing industry. However, the hygiene of farmstead dairy products has not been evaluated. Therefore, the microbiological analysis of farmstead cheeses was performed in this study. Farmstead cheeses (Berg, Colby, Cottage, Gouda, Mozzarella, String, Tilsiter, and Quark) were purchased from 16 dairy farms. In qualitative analysis, the presence of foodborne pathogens (Bacillus cereus, Escherichia coli, Clostridium perfringens, Salmonella, Staphylococcus aureus, Listeria monocytogenes, and Campylobacter spp.) were examined. Also, total aerobic bacteria, Pseudomonas spp., coliform, and E. coli, and yeast/mold were enumerated. Seventeen samples (37.8%) of 45 farmstead cheeses were contaminated with B. cereus and the highest detection rate was observed in String cheese. Two samples (4.4%) were E. coli positive and seven samples (15.6%) were S. aureus positive. Four other foodborne pathogens were not detected in all farmstead cheeses. Also, the mean levels of total aerobic bacteria, coliform, E. coli, and yeast/mold were 4.3 Log CFU/g, 1.4 Log CFU/g, 1.1 Log CFU/g, and 3.8 Log CFU/g, respectively. These results indicate that the food safety of farmstead cheese is extremely poor and, thus, the hygiene management of farmstead cheese should be improved to provide safe farmstead cheese to consumers.