Mate choice, copulation, genital morphology, and sperm storage are not very well understood in millipedes. In particular, the morphology of millipede male genitalia, called gonopods, is critical for genus and species diagnosis in most taxa. However, the external form and function of gonopods vary drastically at the family and ordinal level, complicating morphological comparison across taxa. Three-dimensional x-ray computed tomography (µCT) has provided unprecedented access to internal morphological data, including chitinous sclerites and membranes, muscles, glands, oviducts, and sperm conduits. This work uses µCT data to investigate functional, evolutionary, and developmental aspects of millipede genitalia. First is presented a complete integrated account of morphology and function in the female genital organs (vulvae) in the family Polydesmidae (Diplopoda: Polydesmida), alongside a description of the functional morphology of copulatory interface in the genus Pseudopolydesmus Attems, 1898. This is followed by a comparison of the walking legs and gonopods in Pseudopolydesmus in order to identify homologous elements shared among each type of appendage. Skeletal elements were homologized, but muscle homologies were limited by the dissimilarity of muscle attachment sites between appendage types and by images of juvenile males showing that appendage musculature is totally obliterated once gonopod development begins. Finally, comparative anatomical study of appendage skeletomusculature was extended across a broad swathe of representative millipede taxa. This work included the application of Anatomical Network Analysis to compare the organization of millipede gonopods and walking legs among and within each studied taxon.