External and internal thoracic structures of Nannochorista spp. are described in detail. The results are compared with conditions found in other endopterygote taxa, especially in members of Antliophora. Seventy-seven characters potentially useful for phylogenetic reconstruction are discussed, coded, presented as a data matrix and analysed cladistically. The thorax of Nannochorista shows a number of plesiomorphic characters compared with other mecopterans (except for Merope) and members of the other antliophoran groups (e.g. presence of prospina and associated muscles). No specific affinities of thoracic features of Nannochoristidae and Diptera were found. The cladistic analysis results in strongly supported Antliophora (e.g. intraprofurcal muscle and ventral pleural arms present; bundle of M. mesonoto-pleuralis posterior originates on pleural arm). The thoracic characters do not support the monophyly of Mecoptera. This is possibly an artefact of the analysis. Several potential thoracic autapomorphies of the order are inapplicable in Boreidae, Siphonaptera and Diptera. Boreidae and Siphonaptera share a suite of characters related with flightlessness and are retrieved as sistertaxa when characters associated with wing reduction are predefined as irreversible. Merope appears exceptionally plesiomorphic in its thoracic morphology. Pistillifera (excluding Meropidae) and Panorpoidea (Panorpidae + Panorpodidae) are supported as clades. Due to the strongly modified thoracic morphology of Siphonaptera, the position of this group remains uncertain. The phylogenetic reconstruction using thoracic features alone is clearly impeded by far reaching modifications in Diptera in correlation with an advanced type of anteromotorism, and complex suites of reductional features in the secondary wingless forms.