Autotrophic denitrification (AuDen) is an efficient, convenient and eco-friendly biological process for the treatment of nitrate-contaminated organic-deficient waters. AuDen can be applied as a unique process or complement the conventional denitrification with organics, reducing the risk of organic carbon breakthrough in the effluent and formation of undesirable byproducts downstream (e.g. trihalomethanes). A wide range of inorganic compounds can act as electron donors for AuDen. The most used electron donors include hydrogen gas and reduced sulfur compounds, i.e. elemental sulfur, sulfide and thiosulfate. Recently, the denitrification potential of certain contaminants (such as sulfite, thiocyanate, arsenite and manganese) and inorganic wastes (such as biogenic elemental sulfur from biogas upgrading) has been revealed and attracted interest for developing technologies that combine nitrate removal with water detoxification. This paper critically reviews the state of the art of the most used electron donors for AuDen and highlights recent advances on the application of novel inorganic compounds, reactor configurations and microorganisms to support denitrification. Criteria and guidelines for the selection of a suitable electron donor are provided.