The main goal of our study was to evaluate the effect of the farm, stage of lactation (SL), milking system (MS) and herd size (HS) on somatic cell count (SCC), the total count of microorganisms (TCM) and counts of selected microorganisms (lactobacilli – LBC, Enterobacteriaceae, enterococci, psychrotrophic microorganisms and micromycetes) in sheep milk. An additional part of our study was also the evaluation of the basic composition of milk and the pH of milk. The study was carried out on four selected sheep farms that are situated in the Czech Republic. The means of all traits found on all monitored farms were as follows: SCC – 5.31 log cells mL−1, TCM – 5.24 log cfu mL−1; LBC – 2.98 log cfu mL−1; Enterobacteriaceae – 2.31 log cfu mL−1; enterococci – 2.68 log cfu mL−1; psychrotrophic microorganisms – 4.50 log cfu mL−1; and micromycetes – 2.81 log cfu mL−1. The farm had a significant (p≤0.05) effect only on SCC. The MS had a significant (p≤0.05) effect on SCC and counts of LBC and psychrotrophic microorganisms. In contrast, the SL and HS had no significant effect on SCC, TCM and counts of selected microorganisms. In conclusion, it is necessary to state that all of the detected values of SCC, TCM and selected microorganisms were at a relatively very low level and were also lower than the recommended limits. This fact was, in our opinion, primarily a reflection of regular veterinary checkups and strict adherence to hygiene and sanitation standards. The results obtained are also a good prerequisite for starting the production of dairy products from unpasteurized milk on all monitored farms.