Objective To investigate the microbial and parasitic infection in laboratory mice and rats in Guangdong province from 2013 to 2015.Methods The samples of mice and rats were collected from 12 supervised and 32 entrusting institutions in Guangdong province. The test items and methods were determined according to the national standards, additionally, the test of Helicobacter and Murine Norovirus were added in some samples.Results There were major differences between the results of supervisory test and commission test. There were 4 pathogens detected in mice during the 3-year supervisory tests, including Pseudomonas aeruginosa (0.7%), Pasteurella pneumotropica (0.3%), Klebsiella pneumoniae (0.7%) and Flagellates (1.7%), and with on virus. Meanwhile, only Pasteurella pneumotropica (1.1%) was detected in rats. In contrast, there were 15 pathogens found in commission test of mice, and they were Pseudomonas aeruginosa (3.7%), Pasteurella pneumotropica (5.2%), Mycoplasma spp (1.9%), Staphylococcus aureus (0.7%), Klebsiella pneumoniae (0.8%), Helicobacter (45.3%), MHV (8.5%), TMEV (7.0%), MNV (16.2%), Ect. (0.3%), MVM (0.5%), SV (0.1%), flagellates (11.7%), helminths (1.0%) and ectoparasites (0.1%). At the same time, 8 pathogens were detected in rats, i.e. Pseudomonas aeruginosa (3.4%), Pasteurella pneumotropica (8.6%), Mycoplasma spp (0.9%), Staphylococcus aureus (2.9%), Tyzzer's organism (4.8%), Escherichia coli (1.0%), H-1 (3.0%) and RCV (1.0%). Some pathogens showed high detection ranges and rates, and had characteristics of regional distribution, which could be tested repeatedly in contaminated facilities, such as Pseudomonas aeruginosa, Pasteurella pneumotropica, Helicobacter, flagellates, MHV, TMEV and MNV in mice, as well as Staphylococcus aureus and Tyzzer's organism in rats.Conclusions This study investigated the prevalence and contamination of pathogens in mice and rats in Guangdong province from 2013 to 2015, which provides important references for production, administration, application and revision of standards of laboratory animals.