In recently developed approaches for high-resolution imaging within intact tissue, molecular characterization over large volumes has been largely restricted to labeling of proteins. But volumetric nucleic acid labeling may represent a far greater scientific and clinical opportunity, enabling detection of not only diverse coding RNA variants but also non-coding RNAs. Moreover, scaling immunohistochemical detection to large tissue volumes has limitations due to high cost, limited renewability/availability, and restricted multiplexing capability of antibody labels. With the goal of versatile, high-content, and scalable molecular phenotyping of intact tissues, we developed a method using carbodiimide-based chemistry to stably retain RNAs in clarified tissue, coupled with amplification tools for multiplexed detection. The resulting technology enables robust measurement of activity-dependent transcriptional signatures, cell-identity markers, and diverse non-coding RNAs in rodent and human tissue volumes. The growing set of validated probes is deposited in an online resource for nucleating related developments from across the scientific community. Display omitted •Carbodiimide-based chemistry in CLARITY hydrogels for RNA preservation and detection•Rapid diffusion of DNA oligonucleotides for volumetric in situ hybridization•Detection of microRNAs and mRNAs in clarified mouse and human tissues•DNA-based amplification for multiplexed in situ hybridization in CLARITY CLARITY with enhanced RNA coupling chemistry is developed for multiplexed, volumetric visualization of both long and short RNAs in a variety of intact tissues.