Aldolase C (EC 4.1.2.13) is a brain-specific aldolase isoform and a putative target of the transcription factor HIF-1. We identified Aldolase C as a candidate hypoxia regulated gene in mouse lung epithelial cells (MLE) using differential display. We show that the message accumulates in a robust fashion when MLE cells are exposed to 1% oxygen and is inversely related to oxygen content. Induction in hypoxia is dependent upon protein synthesis. We localize a hypoxia responsive element (HRE) in the aldolase C promoter using a series of deletion and heterologous expression studies. The HRE overlaps with a region of the proximal Aldolase C promoter that is also related to its brain specific expression. The HRE contains an Arnt (HIF-1) and an HIF-1 site. We show that induction in hypoxia is dependent on the HIF-1 site and that HIF-1 protein is present by gel shift assay within nuclear complexes of MLE cells in hypoxia. Aldolase C mRNA expression is developmentally regulated in the fetal lung, rapidly down-regulated in the newborn lung at birth and inducible in the adult lung upon exposure to hypoxia. This pattern of regulation is not seen in the brain. This preservation of this HRE in the promoters of four other species suggests that Aldolase C may function as a stress response gene.