Descriptive morphological studies are often combined with gene expression pattern analyses. Unembedded vibratome or cryotome sections are compatible with in situ RNA hybridization, but spatial resolution is rather low for precise microscopic studies necessary in embryology. Therefore, use of plastic embedding media, which allow semi-thin and ultra-thin sectioning for light and electron microscopy, could be an important advantage. This work suggested a new approach based on the whole mount hybridization of mouse embryos and subsequent epoxy resin embedding. Epoxy resin allowed serial sectioning of semi-thin sections with preserved in situ RNA hybridization signal, which was a necessary prerequisite for precise morphological analysis of embryo development.