Soft x-ray tomography (SXT) is similar in concept to the well-established medical diagnostic technique, computed axial tomography (CAT), except with SXT we obtain images at 50 nm isotropic resolution. We image unfixed, unstained whole cells and obtain contrast by using photons with energies between the K shell absorption edges of carbon (284 eV, λ=4.4 nm) and oxygen (543 eV, λ=2.3 nm), where photons readily penetrate the aqueous environment while encountering significant absorption from carbon- and nitrogen-containing organic material. Since organic material absorbs approximately an order of magnitude more strongly than water, we obtain a unique and quantifiable natural contrast image of cellular structures. X-ray absorption follows Beer’s Law, therefore the absorption of photons is linear, and a function of the biochemical composition at each point in the cell. To date we have used SXT to: 1) reveal sub-cellular consequences of treating pathogenic C. albicans cells with antifungal peptoids; 2) image P. falciparum-infected red blood cells, and the sexual and asexual stages of the parasite; 3) map the structural organization of Saccharomyces cerevisiae during the cell cycle; 4) quantify the changes in chromatin organization during differentiation of mouse olfactory sensory neurons; and 5) show that nuclear aggregation of olfactory receptor genes governs their monogenic expression. To localize specific molecules in intact cells, we recently developed the technology to do correlated fluorescence and x-ray tomography. I will show examples of how these technologies can be used to obtain quantitative information and 3-D views of host – pathogen interactions.