Isolates of Clostridium perfringens from small ruminants in different ecological zones in Nigeria were been investigated to determine the enterotoxin levels in live animals (goats/sheep). A total of 342 fecal samples were collected for the study and out of this number 91 isolates were lecithinase positive. The 91 isolates were characterized into types C and D using the enzyme-linked immunosorbent assay (ELISA). The enterotoxin levels were observed after extensive laboratory analysis using reference strains ATCC 8504D and NCTC 3180C as control. The ELISA method was able to detect as low as 0.1 μg/ml of enterotoxin corrected optical density (OD) at 405 nm, although the values were found to fluctuate with the dilution coefficient. The value of 0.4 OD units was used to estimate the enterotoxin levels of the isolates, and mean value of 0.66 OD units for C. perfringens type D, while the mean value of 0.94 OD units for C. perfringens type C were obtained. It was observed that the sampled animals have high levels of C. perfringen types C and D, which are responsible for causing enterotoxaemia, especially the type D strains. It was also observed that animals having high levels of enterotoxins could move about without showing the signs of illness until found dead or exhibiting the acute form of the disease, enterotoxaemia. This showed the level of tolerant of animals, the West African Dwarf goats and sheep reared in these zones.