We present the clinical applicability of fluorescence ratio reference standard (FRRS) to discriminate different stages of dental caries. Toward this, laser-induced autofluorescence emission spectra are recorded in vivo in the 400- to 800-nm spectral range on a miniature fiber optic spectrometer from 65 patients, with a 404-nm diode laser as the excitation source. Autofluorescence spectra of sound teeth consist of a broad emission at 500 nm that is typical of natural enamel, whereas in caries teeth additional peaks are seen at 635 and 680 nm due to emission from porphyrin compounds in oral bacteria. Scatter plots are developed to differentiate sound teeth from enamel caries, sound teeth from dentinal caries, and enamel caries from dentinal caries using the mean fluorescence intensity (FI) and ratios F500/F635 and F500/F680 measured from 25 sites of sound teeth and 65 sites of carious teeth. The sensitivity and specificity of both the FI and FRRS are determined. It is observed that a diagnostic algorithm based on FRRS scatter plots is able to discriminate enamel caries from sound teeth, dentinal caries from sound teeth, and enamel from dentinal caries with overall sensitivities of 85, 100, and 88% and specificities of 90, 100, and 77%, respectively.