NKp46⁺CD3⁻ natural killer lymphocytes isolated from blood, lymphoid organs, lung, liver and uterus can produce granule-dependent cytotoxicity and interferon-γ. Here we identify in dermis, gut lamina propria and cryptopatches distinct populations of NKp46⁺CD3⁻ cells with a diminished capacity to degranulate and produce interferon-γ. In the gut, expression of the transcription factor RORγt, which is involved in the development of lymphoid tissue–inducer cells, defined a previously unknown subset of NKp46⁺CD3⁻ lymphocytes. Unlike RORγt⁻ lamina propria and dermis natural killer cells, gut RORγt⁺NKp46⁺ cells produced interleukin 22. Our data show that lymphoid tissue–inducer cells and natural killer cells shared unanticipated similarities and emphasize the heterogeneity of NKp46⁺CD3⁻ cells in innate immunity, lymphoid organization and local tissue repair.