Objective To provide substantial data for the choosing of nasopharyngeal carcinoma (NPC) serum diagnostic assays and the quality improvement of commercial kits detecting EBV antibodies. Methods Serum or plasma samples from 33 NPC patients, 30 health donors and 41 non-NPC cancer patients (NNPC) were detected by the commercial kits from 5 different companies for VCA IgA/IgG, EBNA1 IgA/IgG, EA IgA/IgG and Zta IgA detection. Results The specificities of different VCA IgA kits were all high, while the sensitivities were diverse. The sensitivity of the manufacturer A was the highest and the positive agreement rate between the manufacturer A and others was equally low, however the specificity of the manufacturer A was lowest (36.6%) and the manufacturer D ranked first for NNPC. The positive and negative agreements rates between two EBNA1 IgA kits were both high, which were 92.1% and 100% respectively. The sensitivities of EBNA1 IgA kits of the manufacturer B and the manufacturer D were 90.9% and 87.9% each, and the specificities were 96.7% for HD, while 82.9%vand 87.8% for NNPC. The sensitivities of EA IgA were relative low (57.6% for manufacturer A, and 30.3% for manufacturer E) with low positive agreement rate between two kits (39.4%) but the specificities were high (100.0% for manufacturer A and 96.7% for manufacturer E). The sensitivities of VCA IgG of manufacturer A and manufacturer C were 100.0% and 97.0%, and the ones of EBNA1 IgG were similar, but the specificities were quite low except EBNA1 IgG of manufacturer B. Conclusion The differences of diagnostic accuracy and agreement rate between various commercial kits detecting serum or plasma VCA IgA or EA IgA, especially for the manufacturer A and the local products, but not for EBNA1 IgA kits. Three local VCA IgA detection kit showed similar positive results and their sensitivities could be improved further. The proportions of positive results reported by VCA IgG and EBNA1 IgG kits were too high that the cutoff of these products might be modified if using for NPC diagnosis solely.