Background: Our aim was to evaluate the application of the classification of the Papanicolaou Cytopathology Society for the report of biopsies by fine-needle aspiration (FNA) of pancreas and bile duct. Methods: The FNAs obtained consecutively during 1 year were analyzed. Descriptive statistics were performed and sensitivity, specificity, positive predictive value, negative predictive value, and cytohistological correlation were determined. The reference standard test was the histopathological study. Results: A total of 134 cases of FNA were reclassified with ultrasound guidance according to the classification of the Papanicolaou Society, the median age was 59 years (range, 25-80 years). A case interpreted as non-diagnostic was reclassified to category 4 and 3 cases with atypical cells were reclassified to category 5. All malignant cases remained unchanged. Surgical follow-up was performed in 35 patients (26.1%), with a cytohistological concordance in 21 cases (91.3%) and 2 discordant cases (8.7%), the reasons for the discrepancy were due to sampling error, one of them with scarce material to make a diagnosis of higher category, the other case with partial agreement, because cytology was observed atypical cylindrical epithelium, with histology of grade 2 neuroendocrine neoplasia and low grade mucinous intraepithelial neoplasia. In general, the sensitivity and specificity were 100% and 75% respectively, the positive predictive value 88% and the negative predictive value 100%. Conclusions: The FNA guided with endoscopic ultrasound (EUS) and interpreted according to the Papanicolaou Cytopathology Society Classification is an accurate method to evaluate pancreatic and biliary tract lesions with a high positive predictive value of 88%.