In this study, the effect of lactoferrin as an antibacterial activity on the phagocytic activity of E. coli as Gram-negative bacteria and Staph. aureus as Gram-positive bacteria was investigated. The microbiological status of different types of cheese (Kareish, Domiati and Tallaga cheese) was also evaluated. A total of sixty cheese samples (20 samples each) were collected randomly from different markets and restaurants. Pathogenic bacteria including E. coli and Staph aureus were isolated and considered as indicators of the microbiological quality. The effect of lactoferrin on E. coli and Staph. aureus was evaluated to improve the quality of cheese. Lactoferrin antibacterial activity was tested using different concentrations of lactoferrin (zero, 0.5, 1.0, 5.0, 10, and 20 mg/ml) on the survivability of E. coli and Staph. aureus in different varieties of cheese. Lactoferrin showed various inhibition activity on E. coli viability than Staph. aureus, and significantly influenced the count of E. coli in Kareish and Domiati cheese while, and 20% of lactoferrin can inhibit the viability of Staph. aureus in Kareish cheese. Furthermore, their viability in Tallaga cheese was not significantly affected by lactoferrin even by using high concentration. So, lactoferrin could become a promising method to decrease the viability of E. coli and Staph. aureus in cheese.