The incorporation of ontogeny into the interpretation of the vertebrate fossil record promises major advances in palaeontology, systematics, and macroevolution. Here, a key additional component, the incorporation of phylogenetic bracketing into ontogenetic considerations, is demonstrated using cranial anatomy in anguimorphan lizards, a diverse modern clade with an extensive fossil record. The obstacles of fragmentary disarticulated fossil material and low representation in museum collections are overcome by using detailed analysis of individual elements and binning into broad ontogenetic stages, respectively. Results indicate the prevalence of classical macroevolutionary phenomena, notably heterochrony and homoplasy (convergence), throughout anguimorphan evolution. Furthermore, two problematic fossil anguimorph taxa are examined, both of which are unusually small for their clades, suggesting either immaturity or dwarfism. Using extant phylogenetic brackets of ontogenetic trajectories to distinguish between these hypotheses, it is shown that the holotype of one of these taxa is indeed a juvenile (also calling into question its taxonomy) and that the other is a dwarf. It is expected that a phylogenetic approach to ontogeny will yield similar insights across a broad range of fossil and extant organisms. J. Exp. Zool. (Mol. Dev. Evol.) 318B:521–530, 2012. © 2012 Wiley Periodicals, Inc.