Indels are increasingly used in phylogenetics and play a major role in genome size evolution, and yet both the phylogenetic information content of indels and their evolutionary significance remain to be better assessed. Using three presumably independently evolving nuclear gene fragments (28S rDNA, β-fibrinogen, ornithine decarboxylase) from 29 families of neognathous birds, we have obtained a topology that is in general agreement with the current molecular consensus tree, supports the monophyly of Metaves, and provides evidence for the unresolved relationships within the Charadriiformes. Based on the retrieved topology, we assess the relative impact of indels and nucleotide substitutions and demonstrate that the superposition of the two kinds of data yields a topology that could not be obtained from either data set alone. Although only two out of three gene fragments reveal the deletion bias, the combined nucleotide insertion-to-deletion ratio is 0.22, indicating a rapid decrease of intron length. The average indel fixation rate in the neognaths is 2.5 times faster than that in therian (placental) mammals of similar geologic age. As in mammals, there is a considerable variation of indel fixation rate that is 1.5 times higher in Galloanseres compared to Neoaves, and 2.4 times higher in the Rallidae compared to the average for Neoaves (8.2 times higher compared to the related Gruidae). Our results add to the evidence that indel fixation rates correlate with lineage-specific evolutionary rates.