Pancreatic endocrine neoplasm (PEN) and solid pseudopapillary neoplasm of the pancreas (SPN) frequently pose diagnostic challenges. We sought to determine which markers could provide the best immunophenotypic characterization of PEN and SPN, allowing separation on limited cytology samples. We retrieved 22 resected PEN (n = 12) and SPN (n = 10) tumors to serve as a training set for the performance of extensive immunohistochemical staining. Based on these results, we selected a subset of antibodies for application to 25 fine-needle aspiration (FNA) samples from PEN (n = 16) and SPN (n = 9). Chromogranin A, synaptophysin, CD56, and progesterone receptor (PR) highlighted PEN cases in the training set; E-cadherin was noted in a membranous pattern. SPN cases were most immunoreactive for alpha(1)-antitrypsin, vimentin, CD10, and PR, with nuclear staining for beta-catenin; E-cadherin did not show a membranous pattern. Among all FNA samples tested, the immunohistochemical staining of E-cadherin (P = .0003), beta-catenin (P = .00004), and CD10 (P = .00006) demonstrated the greatest difference between PEN and SPN. The pattern of E-cadherin/beta-catenin expression was highly specific for distinguishing PEN from SPN. On limited FNA samples, the characteristic expression of E-cadherin/beta-catenin and the expression of CD10 can be used to distinguish PEN from SPN.