Hypoxia is a feature of most solid tumors and is associated with poor prognosis in several cancer types, including breast cancer. The master regulator of the hypoxic response is the Hypoxia-inducible factor 1α (HIF-1α). It is becoming clear that HIF-1α expression alone is not a reliable marker of tumor response to hypoxia, and recent studies have focused on determining gene and microRNA (miRNA) signatures for this complex process. The results of these studies are likely to pave the way towards the development of a robust hypoxia signature for breast and other cancers that will be useful for diagnosis and therapy. In this review, we outline the existing markers of hypoxia and recently identified gene and miRNA expression signatures, and discuss their potential as prognostic and predictive biomarkers. We also highlight how the hypoxia response is being targeted in the development of cancer therapies.