Here we test the hypothesis that the relationship between egg mass at oviposition (IEM) and incubation period (Ip) is a function of the taxonomic relatedness of bird and reptile species. Allometric relationships between IEM and Ip were examined for 1525 bird species and 201 reptilian species. Treating species as independent data revealed the allometric exponent linking Ip to IEM to be 0.234 for birds and 0.138 for reptiles. However, ANCOVA revealed that within both birds and reptiles the elevation and slope of the regression lines were dependent on the taxonomic order studied, indicating that the exponents were confounded by the phylogenetic relatedness of species. Thus, allometric exponents were recalculated based on the method of comparative analysis using independent contrasts. This technique revealed that the allometric exponent in both birds and reptiles was confounded by phylogeny. In birds the allometric relationship between Ip and IEM was almost halved to 0.122, whereas in reptiles the exponent increased to 0.185. Importantly, the results demonstrate that some results of allometric analyses can be artefacts of the method of analysis of the dataset. That for bird eggs Ip is not determined in large part by egg mass allows new questions to be posed regarding the ecological and physiological factors affecting the length of incubation, and hence rates of embryonic growth, for different taxa and habitats.