Abstract- The higher flies, infraorder Cyclorrhapha [=Muscomorpha (McAlpine, 1989)], have undergone enormous radiation since the Cretaceous (∼100 Myr). Rapid morphological evolution in cyclorrhaphans has made their phylogenetic placement with respect to more primitive clades a long-standing problem in dipteran systematics. Of the two most plausible hypotheses, one treats the Cyclorrhapha as sister group to the orthorrhaphous superfamily Empidoidea [=Empidiformia (Hennig, 1948), Orthogenya (Brauer, 1883)], while the other places them within the empidoids. The debate over cyclorrhaphan origin has heretofore focused on homology interpretations for a few character systems, particularly the male genitalia. We provide the first attempt to assemble and quantify all of the available morphological evidence. By cladistic analysis of these data under alternative codings of genitalic features reflecting opposing homology theories, and then excluding these features altogether, we sought to judge which genitalic theory is better supported by the evidence as a whole, and how much the debate matters to resolving cyclorrhaphan origins. Using the analog of a factorial design, we also measured the effect of alternative transformation series in several other controversial characters, of outgroup choice and of successive weighting. Under all manipulations, including both genitalic codings, the Cyclorrhapha originate within the Empidoidea, near the family Atelestidae. However, trees in which the Empidoidea are constrained to be monophyletic are only 1-6 steps longer (out of ∼150), a fit not significantly worse under a permutation test for monophyly. Adult morphological data may not suffice to settle either the placement of Cyclorrhapha or the debate over genitalic homology. Moreover, the issue of genitalic homology does not appear critical to that of cyclorrhaphan origin.