Understanding developmental processes requires accurate visualization and parameterization of three-dimensional embryos. Tomographic imaging methods offer automatically aligned and calibrated volumetric images, but the usefulness of X-ray CT imaging for developmental biology has been limited by the low inherent contrast of embryonic tissues. Here, I demonstrate simple staining methods that allow high-contrast imaging of embryonic tissues at histological resolutions using a commercial microCT system. Quantitative comparisons of images of chick embryos treated with different contrast agents show that three very simple methods using inorganic iodine and phosphotungstic acid produce overall contrast and differential tissue contrast for X-ray imaging at least as high as that obtained with osmium. The stains can be used after any common fixation and after storage in aqueous or alcoholic media, and on a wide variety of species. These methods establish microCT imaging as a useful tool for comparative developmental studies, embryo phenotyping, and quantitative modeling of development. (c) 2009 Wiley-Liss, Inc.