There is an interaction between feed withdrawal induced-molting and foodborne Salmonella Enteritidis colonization and invasion in susceptible laying hens. Less is known about the ecology of the indigenous microflora and their response to feed removal, the response of S. Enteritidis to feed removal (virulence expression), and the interaction between the gastrointestinal tract microenvironment and S. Enteritidis. Because the crop is the first host environment encountered by S. Enteritidis after ingestion, it can influence the survival and virulence of S. Enteritidis. Feed withdrawal alters the microenvironment of the crop by causing alterations in the indigenous microbial population along with lactate and short-chain fatty acids (SCFA) concentrations and an increase in pH. This altered crop environment is accompanied by increased S. Enteritidis colonization of the crop and ceca along with invasion of the spleen and liver. The observation that crop composition influences the virulence of S. Enteritidis has important implications for understanding the gastrointestinal factors necessary for protection against S. Enteritidis infection. Consequently, an important aspect for minimizing S. Enteritidis colonization during molting is to maintain the crop microflora and their fermentative activities as similar as possible to that of crop microflora and fermentation activities of birds with fully active gastrointestinal microbial populations.