This review discusses some of the recent advances in the characterization of potential vaccine molecules against Schistosoma japonicum, utilizing microscopy and immunocytochemistry methods. Microscopy has demonstrated the stage-specific expression of the muscle protein paramyosin onto the parasite surface, an important consideration as a vaccine target. Other potential vaccine component proteins examined include glutathione S-transferase (GST) and fatty acid binding protein (FABP); although not associated with the adult parasite surface, their localization to internal structures such as lipid droplets and regions of the female reproductive system have provided valuable insights into the biology of the parasite. Localization of the transport protein SGTP (schistosome glucose transporter protein) has demonstrated that the protein is more prevalent in the juvenile stages of the parasite development. This further highlights the diversity of the parasite life cycle. Using both light microscopy and transmission electron microscopy, the localization of a number of schistosome proteins has demonstrated the functions and significance of these proteins within the parasite. Molecular localization studies are crucial in understanding how and when a vaccine may work against the organism and may provide insights into which can be used in the design of future vaccines.