Hypoxia inducible factors (HIFs) are heterodimeric transcription factors that regulate a number of adaptive responses to low oxygen tension. They are composed of alpha- and beta -subunits that belong to the basic helix-loop-helix-PAS superfamily. Here we examined the expression of HIF-alpha subunit proteins in the human kidney and found that, in addition to HIF-1 alpha and -2 alpha, HIF-3 alpha was also expressed. The sequence analysis revealed that, like mouse HIF-3 alpha, human HIF-3 alpha has high similarity with HIF-1 alpha and -2 alpha in the bHLH and PAS domains, but lacks structures for transactivation found in the C-terminus of HIF-1 alpha and -2 alpha. Furthermore, we performed reporter gene analysis and showed that HIF-3 alpha suppresses hypoxia-inducible HIF-mediated gene expression. HIF-3 alpha might be a negative regulator of hypoxia-inducible gene expression in the human kidney.