Squamates (lizards and snakes) include more than 10,000 living species, descended from an ancestor that diverged more than 240 million years ago from that of their closest living relative, Sphenodon. However, a deficiency of fossil evidence 1-7 , combined with serious conflicts between molecular and morphological accounts of squamate phylogeny 8-13 (but see 14 ), has caused uncertainty about the origins and evolutionary assembly of squamate anatomy. We report the near-complete skeleton of a stem-squamate Bellairsia gracilis from the Middle Jurassic of Scotland, documented using high-resolution, synchrotron, phase-contrast tomography. Bellairsia shares numerous features of the crown-group, including traits related to cranial kinesis, an important functional feature of many extant squamates, and those of the braincase and shoulder girdle. Alongside these derived traits, Bellairsia also retains inferred ancestral features including a pterygoid-vomer contact and the presence of both cervical and dorsal intercentra. Phylogenetic analyses return strong support for Bellairsia as a stem-squamate, suggesting that several features that it shares with extant gekkotans are plesiomorphies, consistent with the molecular phylogenetic hypothesis that gekkotans are earlydiverging squamates. We also provide confident support of stem-squamate affinities for the enigmatic Oculudentavis. Our findings indicate that squamate-like functional features of the suspensorium, braincase and shoulder girdle, preceded the origin of their palatal and vertebral traits, and indicate the presence of advanced stem-squamates as persistent components of terrestrial assemblages up to at least the mid Cretaceous. Squamates are among the most speciose of extant vertebrate radiations and are characterised by numerous derived features of both the skull and postcranium. They diversified from an ancestor possessing some or all of these traits, giving rise to taxa as morphologically disparate as snakes, amphisbaenians, chameleons, geckos, and the extinct marine mosasaurs. However, definite stem-squamate fossils representing the early history of the group have until now been rare or absent, spanning from their inferred time of origin in the early Middle Triassic (240 million years ago based on fossils, and older from molecular clock studies 3,15 ), up to the late Early Cretaceous 11,16,17 . This lack of fossil data may explain deep uncertainties regarding the ancestral anatomical states of the squamate crown-group, as evident from conflicts between phylogenetic hypotheses of the relationships among major groups 1,2 . In particular, morphological hypotheses place iguanians as the sister to all other squamates, implying that traits such as presence of a choanal fossa on the palatine, lack of vomerpterygoid contact, vertebral procoely, and loss of distal tarsal 2 are potentially plesiomorphic for squamates 11 . In contrast, molecular phylogenetic hypotheses have consistently resolved iguanians as being deeply-nested, with snakes (Serpentes) and anguimorphs, inste...