Inspired by the emerging new view of animal phylogeny, recent comparative morphological studies have applied the range of available new and established microscopical techniques to shed new light on many received wisdoms about animal evolution. Here I review some illustrative recent work of the participants in the symposium "The New Microscopy: Toward a Phylogenetic Synthesis" held at the annual Society for Integrative and Comparative Biology meeting in San Diego in January 2005. I will discuss 6 case studies. Of these, 3 have generated new morphological insights that are significantly at odds with received wisdom about high-level animal phylogeny but congruent with emerging molecular phylogenies. These examples examine the value of characteristics of arthropod neurogenesis in supporting a controversial new hypothesis of high-level arthropod phylogeny, the insights into annelid phylogeny provided by studies on central nervous system development in clitellates, and how new data on the source of mesoderm in phoronids corroborates their placement in the Lophotrochozoa. The remaining 3 case studies shed new light particularly on the evolution of important innovations that are at the base of successful clades. The examples deal with the evolution of torsion as a major synapomorphy of the gastropods, illustrate how the origin of gastrulation could be studied in sponges, and show that trochophore larvae may characterize a larger clade of spiralians than hitherto suspected.