This study evaluated the isolation, molecular typing and celular proliferation of C. perfringens in small intestine of cattle and sheep distributed in case and control groups. In the case group, out of the 61 bovine samples analyzed, C. perfringens was isolated in 29 (47.54%) and in 4 (33.34%) from 12 sheep samples. In the control group, we did not isolate the microorganism in the bovine samples (73 samples), however it was possible in 5 (20.83%) out of the 24 sheep samples. All isolates (100%) were classified as type A, and cell quantification showed that in control group, all cattle samples resulted in 10 CFU/g of intestinal content while in the study group presented a median value of 104 CFU/g, varying from 10 CFU/g through 108 CFU/g. In ovine group there was a clear divison of values between the two groups. Molecular typing corroborates with other studies regardin the epidemiological importance of type A in enterotoxaemia in ruminants, thus cellular quantification data allow us to conclude that healthy animals present a basal level of C. perfringens lower than 10 CFU/g that does not allow its isolation.