Objective: To analyze reasons for unclear or missed diagnoses in fine needle aspiration biopsy (FNAB) of papillary thyroid carcinoma (PTC). Study Design: Among 35,000 thyroid FNAB diagnoses made during 1989–2009, 135 PTC FNAB diagnoses were divided into 3 categories by expressed probability. A group of 10 cases with histologic PTC diagnosis not mentioned in our previous FNAB sample was also analyzed. Results: Of the 75 PTC FNAB diagnoses, 71 were confirmed; the remaining 4 were hyperplastic goiters. In the group of 45 cases with PTC, in which FNAB diagnosis was the next most probable differential diagnosis, 23 were confirmed. In the group of 15 cases, in which the PTC FNAB diagnosis was considered the less probable differential diagnosis, 3 PTCs were found. The other cases in both groups were usually histologically diagnosed as lymphocytic thyroiditis. In the group of 10 cases with histologic PTC diagnosis, 6 were evaluated as suspicious for (other) malignancy, 3 were diagnosed as hyperplasia with oncocytes and 1 as low cellularity; sample reaspiration was recommended. Conclusion: FNAB diagnosis of PTC is not always possible, with success rate influenced by lesion type and size, accompanying diagnoses, representativeness of cytology sample and experience of the cytopathologist.