RTN3 can recruit Fas-associated death domain (FADD), thus initiating the ER-stress activated apoptosis. It also interacts with the beta-secretase and its aggregation is critically associated with Alzheimer's disease. Here, we first investigated the solution conformation of hRTN3, subsequently characterized its binding with hFADD. The results reveal: (1) both hRTN3 N- and C-termini are intrinsically unstructured. Nevertheless, the C-terminus contains two short helix-populated regions. (2) The unstructured hRTN3 C-terminus can bind to hFADD as shown by ITC. Further NMR investigation successfully identified the binding involved hRTN3 residues. (3) Although upon hRTN3-binding, the perturbed hFADD residues were distributed over the whole sequence, the majority of the significantly perturbed are over its death effector domain, very different from the previously observed binding mode for FADD. This study also implies a possible linkage between Alzheimer's disease and ER-stress activated apoptosis.