Abstract 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. γ‐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.