Fecal RNA method can be used to evaluate biological adaptations of the gastrointestinal (GI) tract of dairy calves through gene expression analysis. A limitation with this method is the current lack of data indicating how the transcriptomic profile observed in fecal RNA mirrors that in specific sections of the GI tract. Therefore, our objective in this study was to compare the transcription of gene markers for GI epithelial cells, fatty acid binding protein 2 (FABP2) and cytokeratin 8 (KRT8) in fecal RNA against several GI tract sections in dairy calves. To test this, postmortem samples were collected from ruminal epithelium, cecum, large intestine, duodenum, jejunum, ileum, and feces from 6 healthy male Jersey calves (5 wk of age) for total RNA isolation. The standard curve was composite from all samples including cDNA from tissues and fecal. The internal control genes used in this experiment were B2M, ACTB, GAPDH, RPS9, RPS15A, and PPIA. Normalized gene expression data were log-transformed before statistical analysis using Proc Mixed of SAS. The expression of FABP2 was greater (P < 0.01) in the duodenum tissue than in GI section associated with fermentation (i.e., rumen, large intestine, and cecum). Within the small intestine the mRNA expression of FABP2 was greater (P = 0.01) in duodenum than in jejunum, but not different than ileum. In fecal RNA, the FABP2 expression was greater (P ≤ 0.03) than in GI section related to fermentation. However, FABP2 was similar (P = 0.3) between fecal RNA and ileum. The expression of KRT8 was greater (P ≤ 0.02) in cecum and large intestine than in rumen and jejunum. Among the small intestine sections KRT8 was greater (P = 0.03) expressed in duodenum than in jejunum. The fecal RNA had greater (P ≤ 0.02) expression of KRT8 than jejunum and ileum. In contrast, the KRT8 expression in fecal was not different than the transcripts observed in cecum and large intestine. Since the transcription of the genes specific for GI epithelial cells were significant observed in the RNA isolated from feces, these preliminary data further confirms that fecal RNA has a potential to be used as a tool to evaluate molecular adaptations in the GI tract of dairy calves.