MRI signal changes in the brainstem are observed in a multitude of disorders including vascular diseases, neoplastic lesions, degenerative diseases, inflammatory disorders, metabolic diseases, infections, and trauma. In some diseases, brainstem involvement is typical and sometimes isolated, while in other diseases, brainstem lesions are only observed occasionally in the presence of other typical extra-brainstem abnormalities. In this review, we will discuss the MRI characteristics of brainstem lesions observed in different disorders associated with frequent and less frequent brainstem involvement. Identification of the origin of the brainstem lesion depends on the exact localisation of the lesion(s) inside the brainstem, the presence and the characteristics of associated lesions seen outside the brainstem, the signal changes on different MRI sequences, the evolution over time of the radiological abnormalities, the history and clinical state of the patient, and other radiological and non-radiological examinations.