Analysis of a comprehensive dataset demonstrates that the brachial index (BI = humerus length/ulna length) of modern birds (Neornithes) varies significantly between clades at all taxonomic levels, yet is strongly correlated with recent phylogenetic hypotheses. Variance in BI at the infraclass level is low, but increases rapidly during the proposed major radiation of neornithines in the Palaeocene and Eocene. Although a BI of greater than 1 is primitive for Neornithes, more basal groups of Mesozoic birds (Confuciusornithidae and some members of the diverse Enantiornithidae) had BIs comparable with those of ‘higher’ modern clades. It is possible that occupation of ecological niches by these Mesozoic clades precluded the divergence of some groups of neornithines until after the Cretaceous–Tertiary boundary. We suggest that with further analysis and data collection the relationships between flight behaviour, ecology and BI can be determined. Hence, BI may provide a useful tool for characterizing the ecology of fossil birds.