In this paper the general features of the neutrino sector in TeV scale quantum gravity theories, such as Arkani-Hamed-Dimopoulos-Dvali (ADD) model and “many species” theory, are investigated. This class of theories has an inherent way of generating small neutrino masses. After reviewing this mechanism it is generalized to a realistic three-flavor case. Furthermore, a procedure is presented on how to diagonalize a mass matrix which is generated by this class of theories and how one can find the Standard Model flavor eigenstates. The developed general approach is applied to two specific scenarios within ADD and many species theory and possible effects on neutrino oscillations and on unitarity of the lepton mixing matrix are calculated. Finally, a short overview of phenomenology which can be potentially testable by the current neutrino experiments is presented.