The invention is directed to a method of treating Alzheimer's disease. The method comprises administering a cysteine protease inhibitor to a patient and thereby affecting the disease. In a preferred method, the cysteine protease inhibitor is a cathepsin B inhibitor. A preferred method causes a reversal in the progression of the Alzheimer's disease, especially an improvement in cognitive deficit. A preferred method also causes a reduction in Aβ. The method includes using a reversible or irreversible cysteine protease inhibitor or a combination thereof.