Clostridium perfringens enterotoxin (CPE) has been implicated as an important virulence factor inC. perfringens type A food poisoning and several non-foodborne human gastrointestinal (GI) illnesses, including antibiotic-associated diarrhea (AAD) and sporadic diarrhea (SPOR). Recent studies have revealed genotypic differences between cpe-positive isolates originating from different disease sources, with most, or all, food poisoning isolates carrying a chomosomal cpe and most, or all, non-foodborne human GI disease isolates carrying an episomal cpe. To evaluate whether these genotypic differences cause phenotypic effects that could influence the pathogenesis of CPE-associated non-foodborne human GI illnesses, a collection of SPOR and AAD isolates has been phenotypically characterized in the current study. All cpe-positive non-foodborne disease isolates examined were found to express CPE in a sporulation-associated manner. The CPE made by these AAD and SPOR isolates was shown to have the same deduced amino acid sequence and toxicity as the classical CPE made by food poisoning isolates. All of the surveyed non-foodborne human GI disease isolates were found to classify as type AC. perfringens, since they produce alpha toxin, but not beta, iota, or epsilon toxins. Finally, no consistent clonal relationships were detected between the surveyed non-foodborne human GI disease isolates. Since, by the criteria examined, all non-foodborne human GI disease isolates examined in this study appear to be phenotypically similar to food poisoning isolates, the current results confirm that the examined AAD and SPOR isolates have enteropathogenic potential. However, given the phenotypic similarities between food poisoning, AAD, and SPOR isolates that have been demonstrated in this study, it remains unclear why the symptomology of non-foodborne human GI diseases is typically more severe and longer-lasting than that of C. perfringens type A food poisoning.