Microfibrils were extracted from human amnion in the form of a beaded filament and analyzed for the presence of transglutaminase-derived cross-links using acrylonitrile derivatization. The cross-link structure was isolated from protease hydrolysates of beaded filaments and identified as a phenylthiocarbamyl amino acid derivative by comparison to a standard. Acid hydrolysis of the isolated cross-link gave the expected lysine and glutamic acid in a 1:1 ratio. The beaded filaments were also treated with trypsin to produce a fraction that contained the bead structure and a fraction containing fragments of the interbead filaments. Cross-links were detected in the interbead filaments but not in the beads. A large tryptic peptide that contained a cross-link was isolated and sequenced. The two amino acid sequences obtained identified both of the cross-linked molecules as fibrillin-1 and enabled the approximate localization of the cross-link sites within the molecule. The locations of cross-link sites on two adjacent molecules fixed the relative positions of fibrillin monomers within the microfibrils, providing insight into the spatial organization of fibrillin within the elastic microfibrils.