In our earlier analysis of Varanus body shape, size was a dominating factor with some qualitative phylogenetic patterns and grouping of species into ecological categories. With a phylogeny and an improved capacity to account for the effects of size, we have reanalysed our morphometric data for male Australian goannas (Varanus spp.) using an increased number of specimens and species to examine whether variations in body shape can be accounted for by retreat choice, as it can for Western Australian Ctenophorus dragon lizards. After accounting for body size in the current analysis, four ecotypes based on retreat choice (i.e. those that retreat to oblique crevices between large rocks or rock faces, those that retreat to burrows dug into the ground, those that retreat to spaces under rocks or in tree hollows, and those that retreat to trees but not tree hollows) accounted for much of the variation in body shape. There is a phylogenetic pattern to the ecotypes, but accounting for phylogenetic effects did not weaken the link between body shape and ecotype based on retreat choice. This suggests that there are large differences in body shape among ecotypes, and shape is relatively independent of phylogeny. The strong link between shape and choice of retreat site in Varanus spp. is consistent with that for Ctenophorus spp. We speculate on why there might be a strong link between retreat choice and body shape for both Varanus and Ctenophorus.