The development of Barrett's esophagus and its progression to adenocarcinoma are clearly linked to reflux of acid and bile. Our objective in this study was to develop an optimized ex vivo biopsy culture technique to study the molecular signaling events induced after insult with individual refluxate constituents. We illustrate the utility of this method by showing results for NF-kB centered cell signaling, and compare the results with those obtained from esophageal cell lines. We show that upregulation of the two NF-kB target genes show differences in pH preference, with IL-8 being preferentially upregulated by DCA at neutral pH, and IkB being upregulated by neutral DCA, acidic DCA, and acid alone. This was found to be true in both cell lines and biopsy cultures. The maximum responses were noted in both models when mixed reflux (DCA at pH 6) was utilized, perhaps reflecting the pH preference of DCA (pKa 6.2). Both the optimized ex vivo models, and the in vitro cell lines show that bile and acid are capable of inducing NF-kB dependent gene expression, with some interesting differences in preferred transcriptional target. In conclusion, in both cells and cultured biopsies, similar reflux driven gene expression changes were noted, with maximum effects noted with DCA exposures at pH 6.