In order to assess the microbiological contamination of laboratory mice and rats in Korea over the 2-year period from 2007 to 2008, we monitored animals housed in mouse and rat facilities equipped with barrier systems. In a barrier animal facility in Korea, the most important viruses in the identified pathogen were the mouse hepatitis virus (MHV) and Pasteurella (Pa.) pneumotropica, and Staphylococcus aureus was identified as the most common bacterial pathogen in Korea. The most commonly detected parasite in the identified pathogen was Trichomonas spp. in the mouse facilities and Entamoeba spp. in the rat facilities. In many cases, these pathogen-contaminated animals were genetically modified animals obtained from the university. Currently, consistent with the increased transfer of genetically modified animals between domestic and foreign animal facilities, the Pa. pneumotropica and parasites infection rates were shown to have increased as compared to those of the 2004-2006 period. Indeed, the MHV infection rate has been maintained at almost 20% in Korean animal facilities over the past 10 years. These results showed that effective quarantine programs for contaminated genetically engineered mutant mice and the monitoring of regular or irregular MHV monitoring in animal colonies should help to reduce pathogen contamination in Korean animal facilities.