The aim of the study is to identify the bacterial agents present in dead baby Guinea pigs from an intensive breeding farm in the district of Manchay, Lima. 191 dead baby Guinea pigs were collected, which were identified and transported at 4 ° C. The processing of the samples was carried out in the Laboratory of Veterinary Microbiology of the Universidad Científica del Sur. The necropsy was performed, taking samples from the liver, intestine, spleen and lung; which were processed in Mc conkey, xylose lysine deoxycholate and blood agar, and the corresponding biochemical tests. The bacterial agents identifyied were E. coli (40.84%), Salmonella spp. (39.27%), among other; at organ level, 32.36% were isolated bacteria in liver, 28.46% in intestine, 20.65% in spleen and 18.54% in lung; showing a significant association (p<0.05) between the bacteriological diagnosis of Salmonella spp. and E. coli, against the evaluated organs.