Endocrine glands are among the organs that most frequently harbor incidentally discovered lesions. Pituitary, thyroid, parathyroid and adrenal incidentalomas are increasingly encountered in everyday practice with variable clinical implications. The major concerns are the risks of malignancy and hormonal hypersecretion mostly in the form of subclinically functioning tumors. Pituitary incidentalomas are usually microadenomas and most of the time clinically unimportant; however, incidentally discovered larger lesions require a more careful diagnostic and therapeutic approach. Thyroid incidentalomas are extremely common; exclusion of malignancy is the main concern in this clinical setting. Although parathyroid adenomas are not uncommon, these lesions are frequently missed owing to their small size and due to clinical unawareness. Adrenal incidentalomas carry a small but finite risk of malignancy. An intriguing challenge regarding incidentally discovered adrenal lesions is that a substantial proportion is associated with hormonal alterations, mainly in the form of subtle cortisol excess. Although still largely controversial, evidence is emerging that so-called subclinical hypercortisolism may not be completely harmless. The best biochemical criterion of subtle cortisol excess remains elusive. Surgical intervention in selected cases results in some beneficial effects, but more data are required in order to routinely support surgery in this clinical setting. This Review provides a brief overview of the prevalence, clinical effect and management of endocrine incidentalomas with a focus on data regarding the diagnostic and therapeutic challenges imposed by incidentally discovered adrenal lesions.