The aim of this cross-sectional study was to investigate associated factors of the severity of clinical mastitis (CM). Milk samples of 249 cases of CM were microbiologically examined, of which 27.2% were mild, 38.5% moderate, and 34.3% severe mastitis. The samples were incubated aerobically and anaerobically to investigate the role of aerobic and anaerobic microorganisms. In addition, the pathogen shedding was quantitatively examined, and animal individual data, outside temperature and relative humidity, were collected to determine associated factors for the severity of CM. The pathogen isolated the most was Escherichia coli (35.2%), followed by Streptococcus spp. (16.4%). Non-aureus staphylococci (NaS) (15.4%) and other pathogens (e.g., Staphylococcus aureus, coryneforms) (15.4%) were the pathogens that were isolated the most for mild mastitis. Moderate mastitis was mostly caused by E. coli (38%). E. coli was also the most common pathogen in severe mastitis (50.6%), followed by Streptococcus spp. (16.4%), and Klebsiella spp. (10.3%). Obligate anaerobes (Clostridium spp.) were isolated in one case (0.4%) of moderate mastitis. The mortality rate (deceased or culled due to the mastitis in the following two weeks) was 34.5% for severe mastitis, 21.7% for moderate mastitis, and 4.4% for mild mastitis. The overall mortality rate of CM was 21.1%. The pathogen shedding (back logarithmized) was highest for severe mastitis (55,000 cfu/mL) and E. coli (91,200 cfu/mL). High pathogen shedding, low previous somatic cell count (SCC) before mastitis, high outside temperature, and high humidity were associated with severe courses of mastitis.