Objective To investigate the feasibitity of detecting S100A6 expression at mRNA level in endoscopic ultrasonography guided fine needle aspiration (EUS-FNA) pancreatic ductal adenocarcinoma (PDA) specimens and its diagnostic value in PDA.Methods A total of 18 PDA specimens and 22 normal pancreatic specimens were collected. RNA was extracted for reverse transcription.The expression of S100A6 gene was examined by real-time polymerase chain reaction.The cut-off value of S100A6 expression at mRNA level in PDA diagnosis was established through receiver operating characteristic (ROC) analysis. 28 patients with pancreatic head masses were selected for EUS-FNA examination,and the value of S100A6 mRNA expression level in PDA diagnosis was prospectively evaluated. The expression of S100A6 protein in PDA tissue was determined by immunohistochemistry staining.Results S100A6 mRNA expression in EUS-FNA and surgical PDA specimens (0.05023±0.10120,0.02083 ± 0.02848) was significantly higher than that of normal pancreatic tissues (0.00164±0.00202),both P＜0.01.The expression of S100A6 in 22 EUS-FNA PDA specimens was significantly higher than that of 6 pancreatic benign disease biopsy specimens (0.00193 ± 0.00278,P =0.0009). There was no significant difference in S100A6 expression between 6 pancreatic benign disease biopsy specimens and normal surgical pancreatic samples (P=0.6143).When S100A6 mRNA expression in EUS-FNA specimens over 0.00525 was taken as positive diagnostic value,the sensitivity,specificity and accuracy in prospective pancreatic cancer diagnosis were 90.01％,100 ％ and 92.85 ％,respectively.Conclusion The high expression of S100A6 mRNA in EUS-FNA specimens of PDA has good preoperative diagnostic value.