The morphological and molecular evidence for higher-level reptile relationships is reassessed. A combined analysis of 176 osteological, 40 soft anatomical, and 2903 (1783 aligned) molecular characters in 28 amniote taxa yields the traditional reptile tree. Synapsids (including mammals) are the sister taxon to all other amniotes, including all extant reptiles. Turtles group with anapsid parareptiles and fall outside a monophyletic Diapsida. Within diapsids, squamates and Sphenodon form a monophyletic Lepidosauria, and crocodiles plus birds form a monophyletic Archosauria. This tree is identical to the tree strongly supported by the osteological data alone when fossils are included. In a combined analysis the strong osteological signal linking turtles with anapsids is sufficient to override a soft anatomical signal placing turtles next to a heterodox archosaur-mammal clade, and a weaker molecular signal linking turtles with archosaurs. However, the turtle-archosaur clade cannot be statistically rejected. When fossils are ignored, the signal in the osteological data set disappears and, in a combined analysis of morphology and molecules, the molecular (turtle-archosaur) signal prevails. These results highlight the importance of fossils, not just in osteological studies, but even in “combined” analyses where they cannot be scored for the majority of characters (soft anatomy and molecules). Although the total number of molecular traits (2903) is much greater than the total number of morphological traits (216), when only characters informative at the relevant levels are considered, the two data sets are approximately equal in size. The partition homogeneity test yields unreliable results unless uninformative (invariant and autapomorphic) characters are excluded. Analyses of the mitochondrial data suggest that recent evidence from nuclear genes for a heterodox turtle-crocodile clade (excluding birds) might be an artefact of inadequate sampling of a diverse outgroup (mammals) and thus, problems with rooting the reptile tree.