Shiga toxin producing Escherichia coli (STEC) is a major cause of food-borne illnesses in humans. This study investigated the presence of STEC in raw milk cheese in Qalyobia Governorate, Egypt. Of totally examined 60 samples (Kareish and Damietta cheeses, 30 of each), 8 (26.7%) and 4 (13.3%) were positive for STEC; respectively. Of 12 isolates, shiga toxin 1 gene (stx1) was detected in 8 samples (66.7%), shiga toxin 2 (stx2) was extracted from all positive samples 12 (100%) while, intimin gene (eae) only from 2 samples (16.7%). Rates of susceptibility of the STEC isolates were detected by using lactoferrin and casein hydrolysates at concentration of 2000 ppm. All isolates were inhibited by LFH while E. coli O26: H11 and O145: H28 were resistance to casein hydrolysate. The LFH reduced STEC O26:H11 and O103:H2 populations by approximately 1.57 and 2.61 log; respectively at 4000 ppm in Kareish cheese during storage period. The antibacterial activity of LFH and casein hydrolysates against STEC revealed by this study indicated that the possibility for application of these protein hydrolysates as natural food preservatives especially against STEC in milk products.