Autopsy data suggests that several brainstem nuclei undergo morphological and molecular changes very early in life, making them an interesting target for the early detection of neurodegenerative diseases. However, imaging these nuclei is not easy, given their size and location. In this talk, I will review the methods that are currently available to structurally image some of these nuclei at the individual level, show some first results and its potential to improve the early detection of Alzheimer's disease. In addition, I will discuss approaches to functionally image these brainstem nuclei, as well the challenges for the future.