In this study simultaneously 6 major mastitis-causing pathogens (Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Staphylococcus epidermidis, Streptococcus uberis, and Escherichia coli), using multiplex-polymerase chain reaction (M-PCR) with self-designed primers were evaluated. Four quarters of the first, third, and fifth parities in industrial, semi-industrial, and traditional dairy cattle farms of Isfahan province in Iran were sampeled. Results revealed a significant effect of farm type on mean somatic cell count (SCC) (P<0.001). A significant difference in mean SCC between different parity levels, but not between different quarters (Left Front, Left Rear, Right Front, and Right Rear) were also observed. M-PCR method could identify 92, 84 and 39% of infected udder quarters with high, medium and low SCC levels. Moreover, the technique facilitates the identification of low levels of pathogens at the start of infection, when the subclinical effects are not yet visible. Compared to contagious pathogens, environmental pathogens showed a higher incidence in quarters with low SCC. Among the pathogens detected by M-PCR, the shares of contagious pathogens in apparently healthy quarters with low SCC, quarters with medium SCC, and quarters with high SCC were 26.3, 45.9, and 50.5%, respectively. Meanwhile, the shares of environmental pathogens in the same quarters were 73.5, 54, and 49.3%, respectively.