Transglutaminase-induced epsilon-(gamma-glutamyl)lysine bonds covalently cross-link and polymerize peptides into insoluble high molecular weight protein aggregates resistant to degradation and proteolytic digestion. We investigated the hypothesis that excessive deposition of epsilon-(gamma-glutamyl)lysine bonds is a neuropathological mechanism which induces the polymerization of tau protein into stable aggregates leading to the formation of paired helical filaments (PHFs) which deposit into neurofibrillary tangles in Alzheimer's disease (AD) brain. We demonstrate a significant (45%) elevation in epsilon-(gamma-glutamyl)lysine cross-links in AD cortex as compared to control cortex. In vivo, PHF tau, and high and medium molecular weight neurofilament proteins have significantly greater cross-linking by epsilon-(gamma-glutamyl)lysine bonds in AD brains as compared to controls. The cross-linking of PHF tau occurs both intra-molecularly and inter-molecularly. The inter-molecular cross-linking of tau could account for the formation of high molecular weight tau polymers. These results suggest that transglutaminase-induced cross-linking of tau protein could play a role in the formation and stabilization of neurofibrillary tangles. Inhibition of transglutaminase-induced cross-linking may therefore, provide a novel strategy for the treatment of AD.