At the International Centre for Diarrhoeal Disease Research, Bangladesh, one-half of the rice-water stool samples that were culture-positive for Vibrio cholerae did not contain motile V. cholerae by standard darkfield microscopy and were defined as darkfield-negative (DF(-)). We evaluated the host and microbial factors associated with DF status, as well as the impact of DF status on transmission. Viable counts of V. cholerae in DF(-) stools were three logs lower than in DF(+) stools, although DF(-) and DF(+) stools had similar direct counts of V. cholerae by microscopy. In DF(-) samples, non-V. cholerae bacteria outnumbered V. cholerae 10:1. Lytic V. cholerae bacteriophage were present in 90% of DF(-) samples compared with 35% of DF(+) samples, suggesting that bacteriophage may limit culture-positive patients from producing DF(+) stools. V. cholerae in DF(-) and DF(+) samples were found both planktonically and in distinct nonplanktonic populations; the distribution of organisms between these compartments did not differ appreciably between DF(-) and DF(+) stools. This biology may impact transmission because epidemiological data suggested that household contacts of a DF(+) index case were at greater risk of infection with V. cholerae. We propose a model in which V. cholerae multiply in the small intestine to produce a fluid niche that is dominated by V. cholerae. If lytic phage are present, viable counts of V. cholerae drop, stools become DF(-), other microorganisms bloom, and cholera transmission is reduced.