We demonstrate that magnetic resonance (MR) microscopy provides a mechanism to investigate normal and abnormal developmental anatomy in a non-destructive and distortion-free manner. Techniques for the fixation, embedding, perfusion and image acquisition of embryos between 3 and 30 mm crown rump length are described. We describe the perfusion of a contrast agent to enhance images of the developing embryonic vasculature. Data are acquired as three-dimensional isotropic arrays which permit images to be reformatted retrospectively in any plane. The data are available for archiving, distributing and for post-acquisition manipulations. MR microscopy is a fast technique for producing three-dimensional reconstructions and is free from registration and sectioning artifacts.