MS has been used to investigate the composition of fibrillin-rich microfibrils from non-elastic and elastic tissues, and to compare fibrillin-1 tryptic fingerprints derived from whole zonules, microfibrils and recombinant fibrillin-1. In all microfibril preparations, fibrillin-1 was abundant and the only fibrillin isoform. MAGP-1 was the only other microfibril-associated molecule. gamma-Crystallin co-purified with zonular microfibrils, so this association may contribute to ciliary zonule anchorage to lens. Recombinant fibrillin-1 tryptic peptides mapped throughout the molecule and included virtually all predicted peptides except for those larger than 4.5 kDa, smaller than 600 Da or post-translationally modified. In contrast, fewer microfibril tryptic fibrillin-1 peptides were detected, although they were derived from domains throughout the molecule and included two peptides after the C-terminal furin processing site. Several microfibril-derived N- and C-terminal domains never yielded any peptides, while tryptic peptides from other domains yielded numerous peptides, suggesting that some tissue microfibril features are retained after trypsinisation. This first MS analysis of a purified extracellular matrix assembly has provided new insights into microfibril composition and fibrillin-1 organisation within them.