The expressions of hypoxia-inducible genes are upregulated by hypoxia-inducible factor 1 (HIF-1), which is a heterodimer of HIF-1alpha and HIF-1beta/ARNT (aryl hydrocarbon receptor nuclear transporter). Under hypoxic conditions, HIF-1alpha becomes stabilized and both HIF-1alpha and ARNT are translocated into the nucleus and codimerized, binding to the HIF-1 consensus sequence and transactivating hypoxia-inducible genes. Other than hypoxia, cobalt and nickel, which can substitute for iron in the ferroprotein, induce the stabilization of HIF-1alpha and the activation of HIF-1. We found previously that, although zinc, another example of a metal substitute for iron, stabilized HIF-1alpha, it suppressed the formation of HIF-1 by blocking the nuclear translocation of ARNT. Here, we identify a new spliced variant of human HIF-1alpha that is induced by zinc. The isoform lacks the 12th exon, which produced a frame-shift and gave a shorter form of HIF-1alpha (557 amino acids), designated HIF-1alphaZ (HIF-1alpha induced by Zn). This moiety was found to inhibit HIF-1 activity and reduce mRNA expressions of the hypoxia-inducible genes. It blocked the nuclear translocation of ARNT but not that of endogenous HIF-1alpha, and was associated with ARNT in the cytosol. These results suggest that HIF-1alphaZ functions as a dominant-negative isoform of HIF-1 by sequestering ARNT in the cytosol. In addition, the generation of HIF-1alphaZ seems to be responsible for the inhibitory effects of the zinc ion on HIF-1-mediated hypoxic responses, because the expressed HIF-1alphaZ behaved in the same manner as zinc in terms of inhibited HIF-1 activity and ARNT translocation.