No past studies of acute diarrhea in Tunisia have examined the phenotypic and genotypic profiles of enterotoxigenic Escherichia coli (ETEC) isolates. We determined 65 ETEC isolates derived from a total of 327 E. coli isolates collected from a previous study (acute diarrheal and healthy persons, children and adults n = 214) and 32 E. coli isolates derived from an acute diarrheal outbreak in Kabaria-Ennour city, Tunis. All E. coli isolates were screened by polymerase chain reaction (PCR) for ETEC virulence genes: sta (heat-stable toxin gene) and elt (heat-labile toxin gene). Seventy-two percent (47 of 65) of ETEC strains expressed the sta gene only, 21.5% (14 of 65) expressed the elt gene and 6.1% (4 of 65) expressed both genes. For the outbreak isolates, the elt gene was predominant (10 isolates out of 14). Ganylioside GM1 enzyme-linked immunosorbent assay (GM1-ELISA) was used to validate the PCR results and this was confirmed by dot blot assay. The same results were obtained. The most common colonization factors (CFs) were CFA/I (44.6%) and coli surface antigen 6 (CS6) (11%), and 44.6% of the isolates showed no association with either CFAs. Resistance of ETEC isolates to tetracycline (38.5%), streptomycin (26%), and beta-lactam agents (ticarcillin 26%, amoxicillin 24.6%, cephalotin 21.5%) was common. Regarding serotypes, the majority of ETEC isolates serotyped as O86:H- (n = 16), O128:H2 (n = 11), and O127:H21 (n = 10). Other serotypes found were O111:H- (n = 6) and O126: H- (n = 5). DNA macrorestriction fragment analysis by pulsed-field gel electrophoresis (PFGE) using the XbaI enzyme was conducted to investigate the epidemiological clonal relationship among ETEC isolates. Major patterns were identified among which some of outbreak ETEC isolates belonged. These data suggest that a proportion of acute diarrhea in Tunis represents the confluence of small epidemics by clonality-related ETEC isolates that are transiently introduced or that persist in our community.