Intrinsic fluorescence (IF) spectra, computed from measured fluorescence emission and diffuse reflectance (DR) spectra, are free from distortions by scattering and absorption. Using an original instrument called FastEEM, white light DR and fluorescence emission spectra generated at 11 excitation wavelengths were collected from heart transplant and autopsy cases. IF spectra were extracted by combining DR and fluorescence spectra using a photon migration model. IF spectra were fit to a linear combination of collagen and elastin spectra at 342 nm excitation, and collagen and component C at 480 nm. C spectrum was derived from multivariate curve resolution analysis and related to ceroid. We calculated contributions of collagen and elastin to IF at 342 and of C at 480 nm, and contribution of beta-carotene absorption to DR. A diagnostic algorithm was derived. Specificity, sensitivity, and validity were verified by leave-one out cross-validation. 110 coronary segments were studied: 22 normal and intimal fibroplasia and 88 atherosclerotic/atheromatous plaques. An algorithm using collagen contribution to IF at 342 nm, contribution of C to IF at 480 nm and that of beta-carotene to DR had sensitivity 95%, specificity 91% and PPV 98%. Fundamental parameters extracted from IF and DR spectra can accurately diagnose atherosclerotic lesions.