We developed the Case Cryo‐imaging system that provides information rich, very high‐resolution, color brightfield, and molecular fluorescence images of a whole mouse using a section‐and‐image block‐face imaging technology. The system consists of a mouse‐sized, motorized cryo‐microtome with special features for imaging, a modified, brightfield/fluorescence microscope, and a robotic xyz imaging system positioner, all of which is fully automated by a control system. Using the robotic system, we acquired microscopic tiled images at a pixel size of 15.6 μm over the block face of a whole mouse sectioned at 40 μm, with a total data volume of 55 GB. Viewing 2D images at multiple resolutions, we identified small structures such as cardiac vessels, muscle layers, villi of the small intestine, the optic nerve, and layers of the eye. Cryo‐imaging was also suitable for imaging embryo mutants in 3D. A mouse, in which enhanced green fluorescent protein was expressed under gamma actin promoter in smooth muscle cells, gave clear 3D views of smooth muscle in the urogenital and gastrointestinal tracts. With cryo‐imaging, we could obtain 3D vasculature down to 10 μm, over very large regions of mouse brain. Software is fully automated with fully programmable imaging/sectioning protocols, email notifications, and automatic volume visualization. With a unique combination of field‐of‐view, depth of field, contrast, and resolution, the Case Cryo‐imaging system fills the gap between whole animal in vivo imaging and histology. histology. Anat Rec, 292:342–351, 2009. © 2009 Wiley‐Liss, Inc.