In microtubules isolated from brains of very old rats, two of the major microtubule-associated proteins, MAP1 and MAP2, are found only in degraded form. MAP1 is present as a piece whose molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis is circa 50,000 smaller than the native protein, and MAP2 is extensively fragmented. The native forms of both proteins are present in tissue homogenates but are rapidly degraded during microtubule isolation. The proteolytic activity responsible for this degradation is cathepsin D like, being more active at acid pH than neutral and being completely blocked by pepstatin at 10(-7) M. Fractionation of aged brain supernatant by gel permeation chromatography showed that the MAP1 and MAP2 degrading activity elutes with a single peak of cathepsin D like activity. MAP1 and MAP2 are known to promote microtubule assembly, and their degradation by a protease whose levels increase with age could be related to defective microtubule assembly which is known to occur in age-related degenerative conditions such as Alzheimer's disease.