Trichuris spp. and Schistosoma spp. are parasitic helminths and causative agents of trichuriasis and schistosomiasis, which affect hundreds of thousands of people worldwide and are significant public health burdens. Using rodent models, microscopy has been a key research tool in understanding the life cycles of these parasites and mechanisms of disease. However, parasites are difficult to find within tissues using sectioning, and 2D microscopy inadequately characterises their complex 3D attachment sites. X-ray micro-computed tomography (microCT) is a relatively new technique in biological research, and allows non-destructive 3D imaging of sample morphology at histological resolutions. This dissertation aimed to exploit the 3D imaging capabilities of microCT to provide novel insights into challenging biological questions surrounding the mouse models of human trichuriasis and schistosomiasis, namely Trichuris muris and Schistosoma mansoni. In order to achieve this, specialised sample preparation, imaging and data analysis workflows were conceived in order to develop and fully exploit the 3D imaging opportunities provided by microCT in the two parasites. Trichuris is a nematode which lives in a highly specialised intracellular "tunnel" made through the epithelial cells of the caecum and proximal colon. At high-levels of infection, Trichuris may cause severe colitis-like symptoms, anaemia and growth retardation. In order to develop new therapies, a greater understanding of the maintenance and formation of the T. muris attachment site is required. 3D MicroCT was used to image the attachment site in toto at histological resolutions. Newly optimised staining of the tissue using osmium tetroxide provided contrast between the worm and the host tissue, and facilitated 3D quantification of the tunnel integrity and the inflammatory status of the host. We identified novel tunnel-forming behaviour in T. muris which contradicts core assumptions pervading the literature and changes the way in which host-parasite interactions might be perceived to occur. In addition, using microCT to steer electron microscopy provided new structural and compositional information on the enigmatic surface structures which cover the anterior-most portion of the worms' surface, suggesting a role for collagen-processing proteins in their formation. Schistosoma mansoni is a vector-borne trematode which lives in the abdominal venules. Schistosome eggs become lodged in systemic organs including the liver and intestine and cause an inflammatory reaction which can cause ascites, colitis-like symptoms and fatal bleeding. However, the manner in which egg-associated blockage and remodelling of liver vasculature contributes to downstream pathology remains poorly investigated. MicroCT was used in order to visualise the development of inflammatory and vascular pathology in the liver during infection, and showed a reduction in vascular branching. Furthermore, total liver inflammation was visualised in 3D, and surprising instances of egg calcification were revealed by a novel correlative imaging approach which used microCT to guide Energy Dispersive X-ray Spectroscopy (EDX). These insights provide an excellent methodological basis from which to quantitatively investigate S. mansoni pathology in future. Overall, the investigations in this dissertation have supplied new insights into the life-cycles and pathologies of Trichuris and Schistosoma infections. Accompanying these are a range of newly developed and refined imaging techniques which may be useful not only in parasitology, but a range of other biological fields.