The male terminalia character system in Diptera is reviewed. The phylogenetic implications of apomorphic changes are traced on published cladograms. New synapomorphies include: anteroventral parameral apodeme for the Tipulomorpha; parameral sheath encompassing desclerotized aedeagus for Neodiptera (exclusive of Axymyiidae); endoaedeagus for Xylophagomorpha + Tabanomorpha. Apystomyiidae are classified as the sister group to the Eremoneura based on four synapomorphies (lateral ejaculatory processes absent, subepandrial sclerite extending from base of hypoproct to phallus, bacilliform sclerites extending to tips of the epandrium and surstyli functionally developed, but not articulated) and lack of eremoneuran synapomorphies (i.e., loss of gonostyli, presence of postgonites and phallic plate). The Diptera sperm pump with a functional ejaculatory apodeme is a possible autapomorphy of Diptera, exclusive of Nymphomyiidae and Deuterophlebiidae. Internal details of the male terminalia of Sylvicola and Mycetobia (Anisopodidae), Hilarimorpha (Hilarimorphidae) and Apystomyia (Apystomyiidae) are newly illustrated and homologies of the aedeagus, paramere and sperm pump of the Tipuloidea are clarified.