Hypoxia is central to both ischaemic and neoplastic diseases. However, the non‐coding transcriptional response to hypoxia is largely uncharacterized. We undertook integrated genomic analyses of both non‐coding and coding transcripts using massively parallel sequencing and interfaced this data with pan‐genomic analyses of hypoxia‐inducible factor (HIF) and RNApol2 binding in hypoxic cells. These analyses revealed that all classes of RNA are profoundly regulated by hypoxia and implicated HIF as a major direct regulator of both the non‐coding and coding transcriptome, acting predominantly through release of pre‐bound promoter‐paused RNApol2. These findings indicate that the transcriptional response to hypoxia is substantially more extensive than previously considered.