Objective To investigate the pathogen infections of Mongolian gerbils raised in a conventional facility, and to provide a basis for the establishment of local standards for pathogen detection in Mongolian gerbils. Methods A total of 16 species of bacteria, 11 species of viruses and 8 species of parasites were detected in 30 gerbils raised in a conventional facility, according to the national standards of microorganism and parasite detection in mice and rats. Results Gerbils raised in this conventional facility were infected with lymphocytic choriomeningitis virus (a positive rate of 6.7%), sendai virus (3.3%), pneumonia virus of mice (100.0%), reovirus type Ⅲ (6.7%), mouse encephalomyelitis virus (10.0%), mycoplasma spp. (6.7%), Tyzzer's organism (6.7%) and Helicobacter spp. (56.7%), according to our antibody detection results. Meanwhile, the detected positive rate of Pasteurella pneumotropica was 3.3%, Staphylococcus aureus 10.0%, Escherichia coli O115 a, C, K (B) 6.7%, Tritrichomonas muris 100.0% and flagellates 100.0%. Conclusions The results of our study provide a reference for the establishment of classification standards for gerbils according to their pathogen and parasite infections.