The impact of molecular biology procedures on neuroendocrine (NE) tumor biology is gradually evolving from purely academic and research studies to clinical applications. This review deals with applications of molecular techniques in neuroendocrine tumors, with special reference to their potential for diagnostic, prognostic, or therapeutic impact. Since the cloning of the genes involved in inherited endocrine tumor syndromes, molecular analysis of the responsible genetic alterations has become a routine diagnostic tool to select affected patients and their relatives, and also an interesting approach to investigate the pathogenesis of neuroendocrine tumors. Assessment of the clonal composition of endocrine tumors could be useful to differentiate hyperplastic versus either adenomatous or carcinomatous conditions, as well as to better understand the clonal relationship between different neoplastic populations in mixed tumors. In addition, molecular approaches allow high sensitivity both in defining the neuroendocrine phenotype in poorly differentiated tumors and in searching for micrometastasis during the follow up of patients with endocrine tumors. Finally, the detection of peptide hormone receptors (e.g., oxytocin and somatostatin receptors) and the development of potent synthetic analogs of such peptides, are opening promising applications in the diagnosis and therapy of endocrine tumors.