Clostridium perfringens enterotoxin (CPE) is responsible for the diarrheal and cramping symptoms of human C. perfringens type A food poisoning. CPE-producing C. perfringens isolates have also recently been associated with several non-food-borne human gastrointestinal (GI) illnesses, including antibiotic-associated diarrhea and sporadic diarrhea. The current study has used restriction fragment length polymorphism (RFLP) and pulsed-field gel electrophoresis (PFGE) analyses to compare the genotypes of 43 cpe-positive C. perfringens isolates obtained from diverse sources. All North American and European food-poisoning isolates examined in this study were found to carry a chromosomal cpe, while all non-food-borne human GI disease isolates characterized in this study were determined to carry their cpe on an episome. Collectively, these results provide the first evidence that distinct subpopulations of cpe-positive C. perfringens isolates may be responsible for C. perfrin-gens type A food poisoning versus CPE-associated non-food-borne human GI diseases. If these putative associations are confirmed in additional surveys, cpe RFLP and PFGE genotyping assays may facilitate the differential diagnosis of food-borne versus non-food-borne CPE-associated human GI illnesses and may also be useful epi-demiologic tools for identifying reservoirs or transmission mechanisms for the subpopulations of cpe-positive isolates specifically responsible for CPE-associated food-borne versus non-food-borne human GI diseases. Clostridium perfringens type A food poisoning currently ranks as the second most common foodborne disease in the United States (2). The diarrhea and cramps that comprise the typical clinical symptoms of this human illness are induced by a single 35-kDa polypeptide named C. perfringens enterotoxin (CPE) (20, 23, 24). Although cpe-positive isolates represent only a very small fraction of the global C. perfringens population (16, 19, 31, 32), recent epidemiologic studies (5-8, 10, 17, 22, 26) indicate that these bacteria can also cause non-food-borne gastrointestinal (GI) illnesses in humans. In particular, some surveys (5, 10, 26) have suggested that CPE-producing C. perfringens may be responsible for 10% of all cases of antibiotic-associated diarrhea (AAD) and 5 to 20% of all cases of sporadic non-food-borne diarrhea (SPOR). Some evidence implicating CPE-producing C. perfringens as a cause of AAD and SPOR includes the following. (i) Feces from many humans suffering from AAD (5, 7, 22) or SPOR (10, 17, 26) contain CPE at levels comparable to those found in feces from C. perfringens type A food-poisoning victims, while CPE is rarely, if ever, detectable in feces from either healthy individuals or individuals suffering from gastroenteritis caused by other en-teropathogens (1, 3, 27); (ii) in the absence of other known enteropathogens, unusually high levels of C. perfringens cells or spores are present in feces from many individuals suffering from AAD or SPOR (7, 10); and (iii) many C. perfringens strains isolated from the fe...