The complexity and variability of the human brain across subjects is so great that reliance on maps and atlases is essential to effectively manipulate, analyze, and interpret brain data. Central to these tasks is the construction of averages, templates, and models to describe how the brain and its component parts are organized. Design of appropriate reference systems for human brain data presents considerable challenges because these systems must capture how brain structure and function vary in large populations, across age and gender, in different disease states, across imaging modalities, and even across species. The authors introduce the topic of brain maps as applied to a variety of questions and problems in health and disease and include a brief survey of the types of maps relevant to mental disorders, including maps that capture dynamic patterns of brain change in dementia.