Primary neuroendocrine carcinomas of the thymus are rare and comprise a wide spectrum of lesions ranging from well-differentiated to poorly-differentiated neoplasms. The classification of such tumors in the thymus is still controversial. By convention, the better-differentiated examples have been traditionally designated as thymic carcinoids and thought to represent the mediastinal counterpart of carcinoid tumors in other foregut locations. However, recent studies have shown that such neoplasms, when arising in the thymus, exhibit a much more aggressive behavior than those originating at other locations. We therefore consider these lesions to represent fully malignant neoplasms that fall within the spectrum of neuroendocrine carcinomas. The designation of well-, moderately-, or poorly-differentiated thymic neuroendocrine carcinoma is therefore favored for these tumors in the present review. Because such tumors may often adopt unusual morphological appearances, it is important to distinguish them from other more common conditions presenting at this location that may exhibit similar histological features. The clinicopathologic, immunohistochemical, and differential diagnostic features of these tumors in the mediastinum are discussed.