Methods and systems for detecting early stage dental caries and decays are provided. In particular, in an embodiment, laser-induced autofluorescence (AF) from multiple excitation wavelengths is obtained and analyzed. Endogenous fluorophores residing in the enamel naturally fluoresce when illuminated by wavelengths ranging from ultraviolet into the visible spectrum. The relative intensities of the AF emission changes between different excitation wavelengths when the enamel changes from healthy to demineralized. By taking a ratio of AF emission spectra integrals between different excitation wavelengths, a standard is created wherein changes in AF ratios within a tooth are quantified and serve as indicators of early stage enamel demineralization. The techniques described herein may be used in conjunction with a scanning fiber endoscope (SFE) to provide a reliable, safe and low-cost means for identifying dental caries or decays.