Human pathogenic viruses such as hepatitis A and E virus (HAV and HEV), which lead to acute liver failure and death, are foodborne pathogens associated with the consumption of virus-contaminated meats, filter-feeding bivalves, fruits, and salads. Two of the three swine farms examined in this study had HAV and HEV positive stool samples in a nested RT-PCR assay. The use of the immunomagnetic separation (IMS) facilitated the separation of HAV through interactions between the ligand on the virion surface and the antibody from the swine feces containing both HAV and HEV. The nested RT-PCR analysis was performed for the detection of HAV obtained from hepatocarcinoma cell line (PLC/PRF/5) contaminated with eluent fraction of IMS. This indicated that IMS has the potential to simultaneously isolate and concentrate target viruses by changing antibodies linked on the magnetic beads.