The aim of this study was to increase understanding of the chemistry involved in the treatment of collagen-rich tissues with glutaraldehyde. Initially 6-aminohexanoic acid (6-AHA) was used to model the lysine/hydroxylysine molecules in collagen before studying the tissue chemistry. Mass spectral data obtained from the reaction of glutaraldehyde with 6-AHA showed the presence of a ,b unsaturated aldehydes (dehydration products of the aldol condensation), and their further condensation products involving Michael reactions with glutaraldehyde, Schiff base cross-links and various cyclization products incorporating pyridinium and dihydropyridine ring structures. The only stable cross-link detected was an ‘anabilysine’-like compound. Similar structures were present in glutaraldehyde-treated tissue. The only detectable stable cross-link identified was anabilysine. No long-chain polymers of glutaraldehyde were detected.