As part of a large-scale study on brain morphometrics and adaptations in mammals, we addressed the problem of chiropteran evolution. A specific statistical framework was designed to test which of two competing hypotheses (bat monophyly vs. diphyly) is more strongly supported by quantitative brain data. Our analyses, based on 120 species, revealed that megabats and microbats were more closely related to each other than to primates, and illustrated the convergent adaptations of the brain of bats to similar trophic (i.e. feeding related) niches. Ecologically-corrected characters were then used to derive a new phylogeny which also supports the chiropteran clade. The monophyletic origin of bats is the preferred hypothesis to explain brain quantitative evolution in chiropterans and primates.