In millipedes, gonopods are male copulatory genitalia derived from walking legs that metamorphose during postembryonic development. The morphology of gonopods is critical for genus and species diagnosis in most taxa. However, the form and function of gonopods vary drastically at the family and ordinal level, making intricate morphological comparison practically impossible. Internal morphology could provide the basis for homologizing morphological elements present in the walking legs and gonopods. Therefore, we used x-ray computed tomography to produce 3D segmentations of Pseudopolydesmus Attems, 1898 (Polydesmida: Polydesmidae) millipedes incorporating two types of morphological elements: skeletal elements and muscles. In addition to imaging the trunk and appendages of an adult male, we imaged the developing gonopod across a series of juvenile male stadia in order to trace the identities of morphological elements. Skeletal elements were homologized, but muscle homologies were limited by the dissimilarity of muscle attachment sites between the walking leg and gonopod. Furthermore, images of juvenile males showed that appendage musculature is totally obliterated once gonopod development begins in the fourth stadium. Due to these limitations, we believe it may be more tractable to homologize gonopod musculature of various millipede taxa to each other than to that of the walking legs. Because distinct genetic developmental networks responsible for walking leg and gonopod patterning have been evolving separately since the common ancestor of gonopod-bearing millipedes (a case of paramorphy), skeletomusculature among gonopods of unrelated millipede taxa is expected to be more similar than that of the gonopod and walking leg within a given millipede lineage.