Hypoxia‐inducible factor (HIF)‐1 and HIF‐2 are heterodimeric transcription factors that mediate the cellular response to hypoxia. Their key regulatory subunits, HIF‐1α and HIF‐2α, 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‐1α or HIF‐2α or both were established. HIF‐1α‐deficient cells displayed lower rates of proliferation and migration, but HIF‐2α‐deficient cells exhibited enhanced anchorage independent growth in a soft agar assay. Xenograft studies revealed that HIF‐1α deficiency inhibited overall tumor growth, whereas deficiency of HIF‐2α stimulated tumor growth. In human colon cancer tissues, expression of HIF‐1α and to a lesser extent, HIF‐2α, was linked to upregulation of VEGF and tumor angiogenesis. However, loss of expression of HIF‐2α but not HIF‐1α was strongly correlated with advanced tumor stage. DNA microarray analysis identified distinct sets of HIF‐1α and HIF‐2α 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‐1α promoted the growth of SW480 colon cancer cells but HIF‐2α appeared to restrain growth. Consequently, therapeutic approaches that target HIF may need to consider these isoform‐specific properties. © 2008 Wiley‐Liss, Inc.