Carrier cattle infected with Babesia bovis and/or Babesia bigemina are difficult to detect because of the low numbers of parasites in peripheral blood. Diagnosis of these carrier status is important for evaluating the efficacies of vaccines and in the epidemiological studies. The present study used the polymerase chain reaction (PCR) to amplify a portion of 644 base pair (bp) of the apocytochrome b gene from both Babesia spp. in one PCR reaction using a common PCR primer pair set conserved in both Babesia spp. and tested the ability of this method to detect the Egyptian strains. The same amplified band was generated and identified by Southern blot hybridization with non-radioactive species specific probes on the Egyptian control samples. The sensitivity of the extra chromosomal DNA-based PCR test was 50 femtogram of DNA / 100 ul extracted genomic DNA of each parasite independently from one ml blood. This was equivalent to one parasite from each species. The PCR assay followed by Southern blot hybridization identified that 30.1% of the carrier cattle harboured B. bovis only and 40.2 % had only B. bigemina as well as 6.02 % had mixed infections with overall rate of 78.3%. Moreover, microscopic examination of blood smears of the same carrier cattle showed the parasites only in 2.4 % of the total samples. This PCR method provides a useful diagnostic tool for detecting carrier cattle infected with B. bovis and/or B. bigemina and the sensitivity is significantly improved over that of current methods. The present investigation also suggest that characteristics of the apocytochrome b gene may make this available target DNA for PCR-based detection of other hemoparasites in Egypt.