In Egypt, to date and to the best of our knowledge, two cases of human babesiosis have been reported; at the same time, very few surveys for detection of B. microti in rodents have been published. These studies were solely relied on microscopic examination of stained blood smears; hence, the molecular confirmative evidence for the presence of B. microti is not revealed. In addition, the epidemiology of human babesiosis, such as competent vectors and reservoirs is still unclear. The present study is a molecular survey of B. microti in wild Egyptian rodents. A total of 30 rodents (26 Rattus norvegicus and 4 Rattus rattus) were collected from different areas in Giza Governorate and tested for Babesia-specific DNA. Nested PCR targeting 18S rRNA gene marker was used to detect the agent in  rodents blood. Positive amplification of 154- bp fragment was detected in 8 (30.8%) R. norvegicus and 1 (25%) R. rattus with atotal prevalence rate of 30%. Unidentified Babesia was detected in 3 rodents (2 R norvegicus and 1 R. rattus) when tested using standard PCR with genus-specific primers. These 3 rodents yielded negative for B. microti. Significant correlation (P<0.05) between positivity to B. microti and splenomegaly was _ found. The difference between the positive rates for B. microti in R. norvegicus and in R. rattus was also revealed to be significant (P<0.05). This study is considered to be the first molecular survey of B. microti in Egyptian rodents.These findings confirm the presence of one of the causative agents of human babesiosis in the country with a relative high prevalence among the suspected reservoir host that warrants more risk for human infections.