To analyze the correlation between rs5029939 locus polymorphism of the tumor necrosis factor ɑ-induced protein 3 (TNFAIP3) gene and myasthenia gravis (MG). Methods: Ninety-eight adult MG patients from northern China (MG group) and 87 healthy controls (control group) were recruited. The polymorphisms were determined by SNPscanTM technique, and results were compared between and within the two groups. Results: There was no statistical difference in the TNFAIP3 rs5029939 locus C/C, C/G, and G/G genotypes nor in frequency of the G allele between the MG group and control group (P>0.05). MG group patients were divided into subgroup according to gender, onset age, concurrent thymoma, anti-acetylcholine receptor (AChR) antibody, and clinical classification, and data analysis showed that the frequency of the G allele in patients negative for the anti-acetylcholine receptor was significant lower than that in patients positive for the anti-acetylcholine receptor (P=0.046, OR=0.328, 95% CI 0.115-0.935). Comparisons between all other subgroups revealed no significant difference (P>0.05). Conclusion: Our result indicate that rs5029939 polymorphism of the TNFAIP3 gene is associated with the expression of the anti-AChR antibody in MG patients.