Cytoprotective heat shock proteins (Hsps) are critical for intestinal homeostasis and are known to be decreased in inflammatory bowel diseases. Signals responsible for maintenance of Hsp expression are incompletely understood. In this study, we find that Hsp25/27 and Hsp70 protein expressions are differentially regulated along the longitudinal length of the large intestine, being highest in the proximal colon and decreasing to the distal colon. This longitudinal gradient was similar in both conventionally colonized mouse colon as well as biopsies of human proximal and distal colon but was abolished in the colon of germ-free mice, suggesting a role of intestinal microbiota in the Hsp regional expression. Correspondingly, analysis of 16S ribosomal RNA genes of bacteria from each colonic segment indicated increased bacterial richness and diversity in the proximal colon. The mechanism of regulation is transcriptional, as Hsp70 mRNA followed a similar pattern to Hsp70 protein expression. Lysates of mucosa-associated bacteria from the proximal colon stimulated greater Hsp25 and Hsp70 mRNA transcription and subsequent protein expression in intestinal epithelial cells than did lysates from distal colon. In addition, transrectal administration of cecal contents stimulated Hsp25 and Hsp70 expression in the distal colon. Thus host-microbial interactions resulting in differential Hsp expression may have significant implications for the maintenance of intestinal homeostasis and possibly for development of inflammatory diseases of the bowel.