Diverse biomolecules within a cel1 emit autofluorescence signals. The assemblage of such signals consists the innate fluorescence signature of a cell, which reflects various cellular properties and also differences in physiological status. We have developed a minimally invasive method (confocal reflection microscopy-assisted single-cell innate fluorescence analysis: CRIF) to optically extract and catalog the innate cellular fluorescence signatures at the resolution of single-cell. CRIF is a promising tool for a streamlined cell analysis, where potential phenotype of each single cell in a heterogenous population is assessed by their autofluorescence signature without invasive cell tagging.