Background: Among life-threatening infections of small ruminants (sheep/goat), enterotoxaemia has vital importance. This disease is caused by certain serotype of Clostridium perfringens and commonly known as pulpy kidney or overeating infection. The current study was carried out to determine the prevalence of C. perfringens in small ruminants in different zones (Kalat, Mangochar, Johan, and Gazg) of district Kalat, Balochistan. Methods: Fecal samples (n=100) were collected aseptically, from rectum of enterotoxaemia suspected animals. The samples were cultured in Reinforced Clostridial Media (RCM). Biochemically identified isolates were further confirmed through polymerase chain reaction (PCR). Result: Overall prevalence of C. perfringens was noticed 48%, with higher occurrence rate (p less than 0.01) in sheep (60%) than goat (36%). Among fifty samples of each specie, 30 and 18 isolates recovered from sheep and goat respectively. The area wise analysis showed that, in goats, the highest prevalence was found in Kalat (50%) followed by the Mangochar (38.46%), Johan (30.77%) and Gazg (25%). The statistical analysis revealed the significant differences (p less than 0.05; 95% confidence interval (CI) 18.80-68.91) in C. perfringens prevalence in various areas of Kalat district. The results of the gender-wise prevalence of C. perfringens exhibited a numerically higher (p greater than 0.05; 95% CI 9.23-49.02) prevalence in female goats (40%) than male goats (32%). Whereas, the age-wise analysis indicated that, in less than 1 year age group (44.44%), the prevalence of C. perfringens was higher (p less than 0.05; 95% CI 8.00-57.89) than greater than 1 but less than 2 years (29.41%) and ³ 2-year (33.33%) age groups. Similarly, in sheep, the highest prevalence (p less than 0.05) was found in Kalat (76.92%) followed by Mangochar (66.67%), Johan (58.33%) and Gazg (38.46%). The age wise and gender-wise differences (p less than 0.05) were also observed in various age and gender groups of sheep similar to goat. Among 30 sheep isolates of C. perfringens, a highest number (28 isolates) showed resistance against amikacin, followed by amoxicillin/penicillin (25 isolates) and colistin sulphate (22 isolates); while among 18 isolates of goat 17 were found resistant against colistin sulphate and 16 were resistant against amoxicillin and amikacin. In conclusion enterotoxaemia is prevailing in small ruminants of district Kalat, Balochistan thus mass scale vaccination campaign should be carried out to prevent losses.