Archaeopteryx brain anatomy was reconstructed using the scan. The reconstruction showed that the regions associated with vision took up nearly one-third of the brain. Other well-developed areas involved hearing and muscle coordination. The skull scan also revealed the structure of its inner ear. The structure more closely resembles that of modern birds than the inner ear of non-avian reptiles. These characteristics taken together suggest that "Archaeopteryx" had the keen sense of hearing, balance, spatial perception, and coordination needed to fly. "Archaeopteryx" had a cerebrum-to-brain-volume ratio 78% of the way to modern birds from the condition of non-coelurosaurian dinosaurs such as "Carcharodontosaurus"
Archaeopteryx be related particularly closely to "Anchiornis" and "Xiaotingia", which were recovered as basal troodontids instead. Agnolín and Novas (2013) found "Archaeopteryx" and (possibly synonymous) "Wellnhoferia" to be the basalmost avialans (Avialae being defined by the authors as including "Archaeopteryx lithographica" and "Passer", their most recent common ancestor and all of its descendants), with Microraptoria, Unenlagiinae, and the clade containing "Anchiornis" and "Xiaotingia" being successively closer outgroups to the Avialae. Another phylogenetic study by Godefroit, "et al.", using a more inclusive matrix than the one from the analysis in the description of "Eosinopteryx brevipenna", also found "Archaeopteryx" to be a member