One of the hallmarks of Alzheimer's disease is the accumulation of amyloid plaques between nerve cells (neurons) in the brain. Amyloid is a general term for protein fragments that the body produces normally. Beta-amyloid is a fragment of a protein that is snipped from another protein called amyloid precursor protein (APP). In a healthy brain, these protein fragments would be broken down and eliminated. In Alzheimer's disease, the fragments accumulate to form hard, insoluble plaques.

Neurofibrillary tangles consist of insoluble twisted fibers that are found inside of the brain's cells. They primarily consist of a protein called tau, which forms part of a structure called a microtubule. The microtubule helps transport nutrients and other important substances from one part of the nerve cell to another (the axon is the long threadlike extension that conducts nerve impulses away from the body of a nerve cell, and dendrites are any of the short branched threadlike extensions that conduct nerve impulses towards the nerve cell body. In Alzheimer's disease the tau protein is abnormal and the microtubule structures collapse.

There is an overall shrinkage of brain tissue as Alzheimer's disease progresses. In addition, the ventricles, or chambers within the brain that contain cerebrospinal fluid, are noticeably enlarged. In the early stages of Alzheimer's disease, short-term memory begins to decline when the cells in the hippocampus, which is part of the limbic system, degenerate. The ability to perform routine tasks also declines. As Alzheimer's disease spreads through the cerebral cortex (the outer layer of the brain), judgment declines, emotional outbursts may occur and language is impaired. Progression of the disease leads to the death of more nerve cells and subsequent behavior changes, such as wandering and agitation. The ability to recognize faces and to communicate is completely lost in the final stages. Patients lose bowel and bladder control, and eventually need constant care. This stage of complete dependency may last for years before the patient dies. The average length of time from diagnosis to death is 4 to 8 years, although it can take 20 years or more for the disease to run its course.