The influence of the source of fermentable material (FM) on the luminal concentrations of their end products and its effects on colon cell metabolism and disease susceptibility is not well characterized. We hypothesized that total fermentation but not the source (type) of FM would be the main factor in determining cellular /molecular outcomes in the healthy colon epithelia. The main aim of this study was to elucidate the role of two different sources of FM, fructooligosaccharides (FOS) and wheat bran (WB), on the expression of genes involved in short chain fatty acid (SCFA) transport, G-protein signaling, apoptosis, cell proliferation and oncogenesis in colon epithelia of healthy rats. Male Fischer 344 rats (n = 10/group) were fed AIN-93G control (0% FM) or experimental diets containing WB (~1%, 2%, or 5% FM) or FOS (~2%, 5%, or 8% FM). Rats were killed after 6 weeks and the colon mucosa was assessed for the expression of target genes using real-time quantitative polymerase chain reaction. By comparison to the control, dose-related changes of mRNA levels were found in rats fed FOS-based diets, including: (a) upregulation of three SCFA transporters (Smct2, Mct1 and Mct4) but downregulation of Mct2, (b) upregulation of Gpr109a and downregulation of Gpr120, Gpr43, Gprc5a, Rgs2 and Rgs16, (c) upregulation of apoptosis-related genes including Bcl2, Bcl2-like 1, Bak1, Caspase 3, Caspase 8 and Caspase 9, (d) downregulation of the oncogenes and metastasis genes Ros1, Fos, Cd44, Fn1 and Plau, and (e) downregulation of several genes involved in cellular proliferation including Hbegf, Hoxb13, Cgref1, Wfdc1, Tgm3, Fgf7, Nov and Lumican. In contrast, rats fed WB-based diets resulted in dose-related upregulation of mRNA levels of Smct2, Rgs16, Gprc5a, Gpr109a, Bcl2-like 1, Caspase 8, and Fos. Additionally, different gene expression responses were observed in rats fed FOS and WB at 2% and 5% FM. Over all, these gene changes elicited by FOS and WB were independent of the expression of the tumor suppressor Tp53. These results suggest that fermentation alone is not the sole determinant of gene responses in the healthy rat colon.