Disclosed are compositions, methods, and kits for clearing tissue that preserve cellular morphology, reporter fluorescence, and epitope labeling which allow for quantitative phenotypic analysis of intact organs. The compositions include, for example, a compound of formula R1—C(X)—NR2R3, wherein R1 is alkyl, haloalkyl, hydroxyalkyl, amino, or alkylamino, X is O or S, and R2 and R3 are independently H, alkyl, or hydroxyalkyl, a salt thereof, or a combination thereof, and at least one non-ionic density gradient medium. Also disclosed are methods for clearing tissue comprising positioning a tissue in a tissue clearing composition and allowing a tissue clearing composition to permeate the tissue. Further disclosed are methods for visualizing tissue characteristics which involve fixing a tissue, staining the tissue, positioning the tissue in the tissue clearing composition and allowing the tissue clearing composition to permeate the tissue, and imaging the tissue utilizing a microscope or tissue scanning device.