Milk is regarded as an important source of essential amino acids, vitamins, and trace elements. Milk from camel is consumed in many Arabian countries as a traditional Medicine. However, few reports investigated the microbiological quality of raw camel milk in a comparison with cattle and buffalo’s milk. This study was conducted to investigate the bacteriological quality of raw milk collected from cattle, buffaloes, and camel. Besides, Isolation and identification of different E. coli serotypes were carried out. Moreover, molecular confirmation of the recovered E. coli isolates via amplification of 16S rRNA and detection of shiga toxin coding genes (stx1, and stx2) were done using PCR. Additionally, the antibiogram of the recovered E. coli isolates was screened using the disk diffusion method. The obtained results indicated that milk samples collected from camels had the lowest microbial counts compared with that of cattle and buffaloes. E. coli was isolated from the collected samples of cattle, buffaloes, and camel at 50%, 20%, and 10%, respectively. Various E. coli serotypes were identified in the present study with the ability of three and four E. coli isolates recovered from cattle milk samples to harbor stx1, and stx2, respectively. All recovered E. coli isolates showed multidrug resistance profiling. Therefore, pasteurization of milk prior to use, and adoption of strict hygienic measures are highly recommended to avoid the risk of human exposure to shiga toxin producing E. coli.