Mucosal tissues are a major site of constant immunological challenge to the host immune system. Here the host must be able to mount protective immune responses against invading pathogenic micro-organisms while, at the same time specifically not activating these mechanisms in response to dietary antigens or the beneficial normal enteric flora. This is achieved in part by innate lymphoid cells (ILCs), a novel family of immune cells that are critical for providing protection against invading antigens in mucosal sites (particularly in the gut), and that play a key role in tissue remodelling and repair after damage from infection or injury. Other ILC family members such as natural killer (NK) cells and lymphoid tissue-inducer cells are critical for virus eradication and lymphoid tissue development, respectively. In a new series of studies, we have dissected the role of key transcriptional factors that control the development of ILC subsets and as such the mutualistic relationship between commensal bacteria and the intestinal immune system which protects against disease.