Objective To conduct a microbiological and parasitological investigation of experimental minipigs in Guangdong province. Methods Four major experimental minipig production units in Guangdong province were included in this investigation. Samples were taken from a total of 154 pigs of 4 brreds, i.e., Bama minipigs, Juema minipigs, Tibet minipigs and Wuzhishan minipigs. Pig fur, scales, serum, rectal swabs and feces samples were collected for detection of 20 pathogens. The data were analyzed and compared among the production units and breeds. Results Mixed infections were detected in all the four institutions. The infection rates of 7 pathogens were rather high:Streptococcus suis type 2 (50.7%), Actinobacillus pleuropneumoniae (40.3%), Mycoplasma hyopneumoniae (100%), Japanese encephalitis virus (41.3%), porcine circovirus type 2 (74.8%), porcine transmissible gastroenteritis virus (73.8%),gastroenteritis virus (44.7%).Porcine parvovirus (26.0%), pseudorabies virus(15.6%) and intestinal worms (3.2%) were also detected in some animals. The immune qualified rates of classical swine fever virus (62.8%) and foot-and-mouth disease virus (35.8%) were rather low. The immune qualified rate of pseudorabies virus was as high as 98.4%. Besides, Salmonella, Brucella, swine dysentery snake like spirochetes, dermatophytes, influenza virus. Toxoplasma gondii, ectoparasites, and coccidia were not detected. Conclusions The results of this investigation indicate that epidemiological quality control of pathogens in experimental minipigs and efforts to establish high grade minipig population in Guangdong province remain to be strengthened. Our study also provides a basis for revision of local and even national standards for experimental minipigs.