Neuromyelitis optica (NMO) and multiple sclerosis (MS) are both autoimmune inflammatory and demyelinating disorders of the central nervous system. Recently, more than 50 MS-susceptibility single-nucleotide polymorphisms (SNPs) have been detected outside the major histocompatibility complex (MHC) region. In this study, we aimed to evaluate the association of these identified non-MHC MS risk loci with Chinese patients with NMO. Thirty-five non-MHC SNPs were selected and genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in 110 NMO patients and 332 controls from southeastern China. Among the 35 SNPs, only one, rs1800693 in the TNFRSF1A locus, was nominally associated with NMO (P = 0.045, OR = 1.550, 95% CI = 1.007-2.384). However, none of the 35 SNPs was associated with NMO after Bonferroni correction. Our results showed no association between these identified non-MHC MS risk loci and NMO, suggesting there are genetic differences in the etiology of NMO and MS.