Objective To detect EPPB41L3 methylation frequency difference between esophageal squamous cell carcinoma (ESCC) tissues and the normal tissues and between ESCC patients′plasma and healthy volenteers′plasma, and to analyze the correlation with clinicopathological parameters. Methods We collected esophageal squamous cell carcinoma tissues (n = 42 patients) and adjacent surrounding normal tissues (n = 42 patients), and plasma from 42 patients with ESCC and from 50 healthy individuals. We used methylation specific PCR (MSP) combined with agarose gel electrophoresis to detect the methylation status of the EPB41L3. We used the SPSS 13.0 software for statistical analysis by χ2 test and Fisher′s exact test. Results EPB41L3 frequency of methylation was significantly higher in tumor tissues than in the adjacent tissues (59.5% vs. 4.8%), the difference was statistically significant (χ2 = 28.873, P < 0.001). For plasma, EPB41L3 methylation frequency was 31.0%in cancer patients, while was not detectable in the healthy volunteers. Methylation of EPB41L3 in tissues was more frequently found in patients with tumor size of ≥ 5 cm or T3 than in patients with tumor size of < 5 cm or T1-2. Conclusions The methylation frequency of EPB41L3 is higher in ESCC tissues than in control normal tissues, and higer in plasma from ESCC patients than that from the healthy volunteers. EPB41L3 methylation is more frequently found in patients with more advanced disease.