An indeterminate diagnosis made on fine-needle aspiration (FNA) samples of the pancreatic lesions can cause dilemmas in clinical management. We retrospectively analyzed FNA features of such lesions in 65 consecutive pancreatic FNAs from 56 lesions to learn more about the sources of uncertainty and their clinical implications. A definitive diagnosis based on follow-up information was available in 50 lesions. Radiologically, 39% of the lesions showed a cystic component, and 25% of the lesions were ill-defined. Cytologically, contributing factors included scant atypical cells, coexistence of gastrointestinal epithelium, pancreatitis, poor cellular preservation, and interpretation error. Repeat sampling, as requested by clinicians prior to treatment, was performed in 33 (66%) of the 50 lesions, leading to a definitive pathologic diagnosis in 20 (61%) lesions. Seventeen lesions were eventually resected, of which a definitive preoperative diagnosis was attempted in 12 lesions via repeat sampling and was successful in seven. We concluded that indeterminate cytologic diagnosis of a pancreatic lesion often needs to be pursued for optimal management. Although intrinsic natures of a lesion such as cystic component may contribute to insufficient sampling, diagnostic certainty can be improved by proper specimen handling, interpretation, and clinical and/or radiographic correlation.