The aim of this study was to identify bacterial agents isolated from fatal cases in Guinea pigs as well as to evaluate their antibiotic susceptibility from two commercial-family breeding centres in the province of Canchis, Cusco-Peru. In total, 230 animals (130 with respiratory lesions and 100 with enterohepatic lesions) were processed, including samples of the liver, lung, spleen and intestine. A microbiological culture and antibiogram were performed on agar with discs of the main antibiotics used in Guinea pigs rearing. In the respiratory lesions, Streptococcus sp (47.1%), Bordetella sp (26.4%), Salmonella sp (13.8%), Klebsiella sp (9.2%) and Pasteurella sp (3.4%) were identified. Likewise, in Guinea pigs with enteric lesions, Salmonella sp (56.8%), E. coli (29.7%), Citrobacter sp (7.6%) and Klebsiella sp (5.9%) were identified. The highest frequency of bi-bacterial isolates in respiratory lesions was for Streptococcus sp and Bordetella sp, while for liver-enteric lesions it was Salmonella sp and E. coli was registered. The general frequency of resistance in the isolates was 5.4 and 3.6% for enrofloxacin and trimethoprimsulfamethoxazole, respectively. The results showed a variety of bacterial genera present in respiratory and enteric-hepatic processes in Guinea pigs, as well as a low frequency of antibiotic resistance in the isolated strains.