Description: Influence of breed on somatic cell count (SCC) and occurrence of particular species was evaluated. The samples were collected from farms with Holstein (H; 10 farms - 365 cows) breeding and from farms with Czech Fleckvieh (CF; 2 farms - 67 cows). The obtained dataset was statisticaly evaluated by analysis of variance. The occurrence of pathogens was compared between H and CF. The relationship between SCC and incidence of pathogens was determined as well. It is evident that more positive cows were in breed H compared to CF (H 41.6 PROCENT ; CF 26.9 PROCENT ). The most frequent pathogens in H breed were S. aureus(13.7 PROCENT ), S. uberis (9.6 PROCENT ), S. haemolyticus (8.5 PROCENT ), S. agalactiae (6.9 PROCENT ), E. faecalis (2.5 PROCENT ) and E. faecium (0.8 PROCENT ), while only S. uberis (19.4 PROCENT ), S. haemolyticus (6 PROCENT ) and S. aureus (1.5 PROCENT ) were found in CF. SCC results showed the higher SCC in H breed in case of both negative and positive cows as well and significant impact of breed on logSCC (F = 6.4, P = 0.012). The significant effects of bacterial species were confirmed (F = 13.6, P < 0.001). Multiple comparison among groups of bacterial species showed significant differences between negative and S. aureus, S. agalactiae, S. uberis (P = 0.012, P < 0.001, P < 0.001). Differences between negative and other pathogens were not signifiant