Heat stressed cattle have depressed feed intake. However, performance reductions observed during heat stress are greater than could be expected from depressed intake alone. This disparity suggests that digestive, absorptive, or post-absorptive shifts in physiology may also influence the degree to which animals respond to heat stress. Our objective was to investigate the effect of heat stress on the expression of genes in the rumen epithelium associated with the transport and metabolism of volatile fatty acids (VFA), testing the hypothesis that absorptive function of the epithelium is impaired by heat stress. Eight ruminally cannulated Holstein heifers (200 kg) were used in a factorial, repeated measures experiment with 2 treatments and 2 periods. During the first period, animals were provided feed ad libitum and housed at 20°C. During the second period, one group (HS) was housed at 30°C and fed ad libitum. The other group (PF) was housed at 20°C and pair-fed to match the intake of heifers in the HS group. During each period, animals were exposed to the heat or intake treatment for 9 d and the 10th d of each period was used for papillae biopsy sample collection. During the second period, indicators of heat stress including feed intake, respiration rate, heart rate, and body temperature were significantly different between PF and HS animals (P < 0.05). There was a significant feed intake effect on BHD1 expression (P = 0.04), and a tendency for a heat stress effect (P = 0.08), with expression increasing in both cases. This data indicates increased β-hydroxybutyrate production. Differential expression of epithelial transporters responsible for VFA uptake into the epithelium (MCT4 and NH3), and transport into the blood (NHE1 and NHE2) was observed. Expression of MCT4 was significantly affected by feed intake (P = 0.003) as were all NHE genes (NHE1, NHE2, and NHE3; P < 0.05). These results indicate that both heat stress and feed intake can affect gene expression in the rumen epithelium. With low feed intake, the epithelium appears to increase capacity for VFA absorption and transport. However, during heat stress, it appears that butyrate metabolism and transport capacity is decreased.