Objective To examine the single nucleotide polymorphism(SNP) of apurinic/apyrimidinic endonuclease1 (APE1) in primary small cell carcinoma of esophagus(PSEC) ,then investigate the relationship between these SNPs and the prognosis.Methods Sixty cases first-treated patients with PSEC were recruited, patients with esophageal squamous cell carcinoma (ESCC) and healthy blood donors were recruited as positive and negative controls.APE1 (Asp148Glu) of the patients with PSEC and controls were genotyped by the TaqMan method.Every patient was treated with platinum-based chemotherapy(EP regimen for PSEC and TP regimen for ESCC)and radiotherapy(3D-CRT) ,then every case was followed-up for 2 years.The relationship between these SNPs and the follow-up outcome was analyzed.Results Compared with the ESCC group and control group, APE1 148 pure mutant(Glu/Glu) of PSEC group increased significantly(PSEC group was 40％ (12/30), ESCC group was 13.3％ (4/30) , control group was 10％ (2/20)), the difference was statistically significant (x2 =7.248,P =0.027).According to data of following-up, there was a significant increase in rate of progress (1year:40.0％ (12/30) vs 16.7％ (5/30), x2 =4.022, P =0.045;2 years: 86.7％ (26/30) vs 40.0％ (12/30) ,P =0.004) and a significant decrease in survival (33.3％ (10/30) vs 76.7％ (23/30)) of PSEC compared with ESCC.The SNPs of APE1 Asp148Glu was significantly correlated with frequency of progress, a significant increase was found in rate of progress of the patients with mutant type(Asp/Glu±Glu/Glu) compared with wild genotype(1 year: 50.0％(11/22) ,x2 =3.854,P=0.05;2 years: 81.8％ (19/22) ,x2 =10.519,P =0.001) ,the survival of the patients with mutant genotype was significantly lower than wild type (22.7％ (5/22) ,x2=10.77,P=0.001).Conclusion The most of polymorphisms of APE1(Asp148Glu) are mutation type in PSEC.Pure mutant genotype (APE1 148Glu/Glu) carry significant enhancement of progression.The polymorphisms of APE1 (Asp148Glu) maybe one of those molecular mechanisms of high frequency of progress and poor prognosis in PSEC.