We welcome Naito et al.'s recent efforts to gain greater information about the diet and ecological niche of Neanderthals, through compound-specific amino acid nitrogen isotopic analysis of bone collagen from Neanderthal remains from Spy Cave in Belgium as well as of specimens of contemporary animal species (Naito et al., 2016a). The application of a relatively novel technique (see: Styring et al., 2010, Chikaraishi et al., 2014, McMahon and McCarthy, 2016) is not without its problems, and we would like to provide a critical comment on the implications of uncertainties for the interpretation and application of this method, and on analytical aspects of this technique.