Toxigenic Vibrio cholerae strains are lysogens of CTX, a filamentous bacteriophage which encodes cholera toxin (CT). Following infection of recipient V. cholerae cells by CTX, the phage genome either integrates into the host chromosome at a specific attachment site (attRS) or exists as a replicative-form (RF) plasmid. We infected naturally occurring attRS-negative nontoxigenic V. cholerae or attenuated (CTX attRS negative) derivatives of wild-type toxigenic strains with CTX and examined the diarrheagenic potential of the strains carrying the RF of the CTX genome using the adult rabbit diarrhea model. Under laboratory conditions, strains carrying the RF of CTX produced more CT than corresponding lysogens as assayed by a G_M1-based enzyme-linked immunosorbent assay and by fluid accumulation in ligated ileal loops of rabbits. However, when tested for diarrhea in rabbits, the attRS-negative strains (which carried the CTX genome as the RF) were either negative or produced mild diarrhea, whereas the attRS-positive strains with integrated CTX produced severe fatal diarrhea. Analysis of the strains after intestinal passage showed that the attRS-negative strains lost the phage genome at approximately a fivefold higher frequency than under in vitro conditions, and 75 to 90% of cells recovered from challenged rabbits after 24 h were CT negative. These results suggested that strains carrying the RF of CTX are unable to cause severe disease due to rapid loss of the phage in vivo, and the gastrointestinal environment thus provides selection of toxigenic strains with an integrated CTX genome. These results may have implications for the development of live V. cholerae vaccine candidates impaired in chromosomal integration of CTX. These findings may also contribute to understanding of the etiology of diarrhea occasionally associated with nontoxigenic V. cholerae strains.