Alzheimer's disease - Causes. Causes of Alzheimer's disease. Alzheimer's disease is caused by parts of the brain shrinking (atrophy), which affects the structure and function of particular brain areas. It's not known exactly what causes this process to begin. However, in the brains of people with Alzheimer's disease, scientists have found amyloid plaques (abnormal deposits of protein), neurofibrillary tangles (containing tau) and imbalances in a chemical called acetylcholine.