Results from a comparative anatomical study of the mesosomal skeleton of Chalcidoidea are presented. External and internal features are described and illustrated for 39 chalcidoid taxa, representing 16 families and 29 subfamilies. This is the most comprehensive morphological study ever conducted for the superfamily. The mesosoma was dissected, macerated and investigated using scanning electron microscopy. The mesothorax and metathorax contributed most of the phylogenetically relevant information. The metafurca is highly variable within Chalcidoidea but seems to be relatively constant at the subfamily level. One hundred and fifty-four morphological characters were scored and analysed cladistically. Outgroup species were chosen from six apocritan superfamilies: Stephanoidea, Ceraphronoidea, Cynipoidea, Platygastroidea, Proctotrupoidea and Mymarommatoidea. Some previously suggested chalcidoid relationships were retrieved: (1) Pteromalidae: Pteromalinae + Miscogasterinae + Panstenoninae; (2) Perilampidae + Eucharitidae; (3) Chalcididae + Leucospidae + Eurytomidae; (4) Eulophidae: Eulophinae + Tetrastichinae + Entedoninae; and (5) Eupelmidae + Encyrtidae. Mymarommatoidea renders Chalcidoidea paraphyletic in our analyses; however, the taxon sample is too restricted to provide a robust hypothesis. Three previously unreported putative autapomorphies of Chalcidoidea were revealed: (1) presence of an exposed, triangular or diamond-shaped prosternum; (2) presence of a percurrent mesopleural sulcus anteriorly terminating in the acropleuron; and (3) presence of paired metapectal plates lateral to the metafurca.