Hypoxia-inducible factor (HIF)-1 and HIF-2 are heterodimeric transcription factors that mediate the cellular response to hypoxia. Their key regulatory subunits, HIF-1alpha and HIF-2alpha, are induced similarly by hypoxia, but their functional roles in cancer may be distinct and isoform-specific. SW480 colon cancer cells with stable expression of siRNA to HIF-1alpha or HIF-2alpha or both were established. HIF-1alpha-deficient cells displayed lower rates of proliferation and migration, but HIF-2alpha-deficient cells exhibited enhanced anchorage independent growth in a soft agar assay. Xenograft studies revealed that HIF-1alpha deficiency inhibited overall tumor growth, whereas deficiency of HIF-2alpha stimulated tumor growth. In human colon cancer tissues, expression of HIF-1alpha and to a lesser extent, HIF-2alpha, was linked to upregulation of VEGF and tumor angiogenesis. However, loss of expression of HIF-2alpha but not HIF-1alpha was strongly correlated with advanced tumor stage. DNA microarray analysis identified distinct sets of HIF-1alpha and HIF-2alpha target genes that may explain these phenotypic differences. Collectively, these findings suggest that HIF isoforms may have differing cellular functions in colon cancer. In particular, HIF-1alpha promoted the growth of SW480 colon cancer cells but HIF-2alpha appeared to restrain growth. Consequently, therapeutic approaches that target HIF may need to consider these isoform-specific properties.