Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone-binding proteins that regulate transcriptional responses to peroxisome proliferators and structurally diverse fatty acids. PPARs have been implicated in a wide variety of functions, including lipid homeostasis and inflammatory responses. In this study, we examined the expression of PPAR-alpha in response to ambient hypoxia. Initial studies using microarray analysis of intestinal epithelial mRNA revealed that hypoxia rapidly down-regulates PPAR-alpha mRNA and protein in epithelial cells in vitro and in vivo. Subsequent studies revealed that the PPAR-alpha gene bears a DNA consensus motif for the transcription factor hypoxia-inducible factor 1 (HIF-1). EMSA analysis revealed that ambient hypoxia induces HIF-1alpha binding to the HIF-1 consensus domain of PPAR-alpha in parallel to HIF-1 nuclear accumulation, and antisense depletion of HIF-1alpha resulted in a loss of PPAR-alpha down-regulation. The PPAR-alpha ligand pirinixic acid (WY14643) functionally promoted IFN-gamma-induced ICAM-1 expression in normoxic epithelia, and this response was lost in cells pre-exposed to ambient hypoxia. Such results indicate that HIF-1-dependent down-regulation of PPAR-alpha may provide an adaptive response to proinflammatory stimuli during cellular hypoxia. These studies provide unique insight into the regulation of PPAR-alpha expression and, importantly, provide an example of a down-regulatory pathway mediated by HIF-1.