The projection X-ray microscope utilized a very small X-ray source emitted from a thin (0.1-3 μm) target metal film excited by the focused electron beam of a scanning electron microscope (SEM). When an object is placed just below the target metal film, the diverging X-rays enlarge the shadow of the object. Because no X-ray optics such as a zone-plate is used, the focal depth is, in principle, infinitely large. We exploited this to apply projection X-ray microscopy to three-dimensional (3-D) structure analysis by means of cone-beam computed tomography (CT). A small arthropod (Pseudocneorhinus bifasciatus, 5 mm in length) was examined for CT study. The projection images were recorded at 3-degree increments over the whole range (360°) of a stepping-motor- controlled sample rotator. The 3-D reconstructed image was calculated to be 256 × 256 × 256 (5 μm) voxel data. The reconstructed 3-D image showed in detail the internal structure of an opaque object. Trial for element mapping using projection X-ray microscope is also performed by developing a new target exchanger. This apparatus enables exchange of metal targets without leaking vacuum of SEM. By taking images using Ka line from nickel and cobalt targets, distribution of iron, which has absorption edge between two Ka lines, can be shown. Distribution of less than 10 μm iron particles is distinguished from cobalt particles. This system would be applicable for 3-D element analysis.