Neuromyelitis optica (NMO) is an inflammatory autoimmune demyelinating disease of the central nervous system (CNS). NMO autoantibodies (NMO-IgG) recognize the glial water channel Aquaporin-4 (AQP4). In the plasma membrane AQP4 is able to form typical supra-molecular structures named orthogonal arrays of particles (OAPs). We recently demonstrated that NMO-IgG epitope is intrinsic in AQP4 assemblies into the extracellular surface of the OAPs. To identify the AQP4-OAP extracellular epitope for NMO IgG, we generated a series of AQP4 mutants in the three extracellular loops (A, C and E) and the binding capacity of NMO sera was tested by immunofluorecence and immunoprecipitation. Results indicate that one group of sera was able to recognize the amino acid sequence G₁₄₆VTTV₁₅₀ (extracellular loop C), and a second group of sera was characterized by a predominant role of the amino acids G₆₁SEN₆₄ (extracellular loop A). However, for both groups, the binding capacity was further reduced when these amino acids were mutated together with those in loop E suggesting a conformational epitope. Our data indicate that the NMO-IgG autoantibodies have a polyclonal origin and that the three AQP4 extracellular loops (A, C, and E) participate in the formation of the NMO-IgG epitope. This study identifies two major key immunodominant conformational epitopes and provides crucial information for the generation of a NMO disease model.