Cytology is an easily-accessible, cost-effective, and safe procedure for the initial evaluation of most endocrine/neuroendocrine lesions. Both fine-needle aspiration cytology and exfoliative cytology have shown good sensitivity and specificity in detecting endocrine/neuroendocrine benign proliferations and malignancies. Thanks to its utility for early diagnosis, cytology has contributed to the decline in mortality of endocrine/neuroendocrine neoplasms. The endocrine system comprises different endocrine organs, such as the thyroid, adrenal glands, paraganglia, parathyroid, pancreas, hypothalamus, pituitary gland, ovaries and testes, which can give rise to non-neoplastic, benign and malignant proliferations. In addition, several neuroendocrine cells do not form specific endocrine organs, but are widely present along other systems, notably in the lungs and in the gastrointestinal tract. The general diagnostic approach to proliferations originating from neuroendocrine cells is similar to that of endocrine organs. This review focuses on the cytological features of neuroendocrine proliferations, with particular emphasis on their most common sites of origin, i.e. the thyroid, pancreas, lungs and skin. Ancillary approaches applied to cytological material to improve diagnosis will also be discussed.