Summary Objective: Endoplasmic reticulum aminopeptidase 1 (ERAP1) is known to participate in the pathogenesis of ankylosing spondylitis (AS) cooperated with HLA-B27. This study aimed to evaluate the relationship between promoter methylation and mRNA levels of ERAP1 and AS. Methods: The DNA methylation level of 100 AS patients and 100 health controls (HCs) were tested using targeted bisulfite sequencing assay. Besides, the mRNA level of 20 AS patients and HCs was measured used quantitative real-time reverse transcription-polymerase chain reaction to verify the results of DNA methylation. Results: The methylation levels of two CpG islands containing 31 loci in ERAP1 promoter were measured. ERAP1_1 (P < 0.001) and ERAP1_2 (P < 0.001) islands were significantly hyperrmethylated in AS patients compared with healthy controls. Correspondingly, the mRNA level was significantly lower in AS patients. The ROC curve analysis reported the sensitivity, specificity and area under curve were 0.717, 0.737 and 0.779 of differential methylated CpG loci of ERAP1 for AS diagnosis. Besides, we also found that the methylation level was associated with the family history, non-steroidal anti-inflammatory drugs use, X-ray classification and clinical manifestations. Conclusions: Our study demonstrated that the ERAP1 gene is significantly hypermethylated in AS patients, which is verified by the lower mRNA level of AS patients. Our findings suggested that aberrant methylation of ERAP1 promoter may take part in the pathogenesis of AS and can be considered as diagnostic tool and therapeutic target of AS.