Pathogenic isolates of Clostridium perfringens were identified in lambs and kids population from non-vaccinated dams of selected districts of Khyber Pakhtunkhwa province, Pakistan. Samples were obtained from non-vaccinated lambs and kids with the signs of enterotoxaemia. The isolates were initially identified by colony characteristics, Gram staining, biochemical tests and CFU/g. Clostridium perfringens was isolated from 43.45% of lambs and 50.59% of the kids. Obtained isolates were further analyzed for toxinotyping with conventional PCR. Sequence analysis of 73 strains from diseased lambs showed 13.10% type A, 9.52% type B and highest 20.83% proportion of Clostridium perfringens type D. Out of 108 strains from kids, 54.62% were type A, 9.25% were type B and 36.11% were type D. Clostridium perfringens type C and E were neither detected in lambs nor in kids. The association of various factors (i.e. area, housing, seasons, colostrum feeding, hygienic condition, body condition and animal sex) with each type of Clostridium perfringens infection were analyzed by Chi- square test of association (χ2). The results indicated that Colostrums feeding, hygienic condition and body condition scores of animals are significantly (P<0.05) associated with Clostridium perfringens type A, B and D in both lambs and kids. Besides that, Season with Clostridium perfringens type A in kids, Area and Season with Clostridium perfringens type D in lambs are also significantly (P<0.05) associated.