We present a broadly applicable procedure for whole-mount imaging of antibody probes in embryonic tissues at microscopic resolutions based on combining a metal-based immunodetection scheme with x-ray microtomography (microCT). The method is generally accessible, relying on standard enzyme-conjugated secondary antibodies and other readily available reagents, and is demonstrated here with microCT visualizations of acetylated α-tubulin in the chick nervous system and of type II collagen in developing limbs. The tomographic images offer complete three-dimensional representations of molecular patterns obtained with immunostaining methods at the level of organ development, with added possibilities to quantify both spatial distributions and varying densities of gene products in situ. This imaging modality bridges a crucial gap in three-dimensional molecular imaging by combining the histological resolutions of confocal microscopy with a greater specimen size range than optical projection tomography, and thus enables a powerful new approach to long-standing issues of skeletogenic pattern formation in vertebrate limbs. Developmental Dynamics 240:2301–2308, 2011. © 2011 Wiley-Liss, Inc.