Stokes Shift Spectroscopy (S3) offers a novel way to rapidly measure spectral fingerprints of complex molecular mixtures in tissue. The changes of key fluorophores from normal state to the malignant state can be reflected by alteration of Stokes Shift Spectra (S3 spectra). S3 measuremen ts can be used to acquire en ough information of different key fluorophores from one spectrum to speed up spectral acquisition time. In this study, we demonstrate the usefulness of the S3 technique to distinguish the malignant tissue from the normal prostate and breast tissues. The optimal wavelength shift constant ( 'O c ) of S3 spectra measurements for prostate/breast cancer detection were determined to be 40 nm. The underlying physical and biological basis for S3 is discussed. For the first time, our work explicitly discloses how and why S3 is supreme in comparison with other conventional spectroscopic techniques. Keywords: Cancerous human breast tissue, Stokes Shift Spectroscopy (S3), tryptophan, collagen, and NADH 1. INTRODUCTION Optical spectroscopy and imaging provide powerful tools for non-invasive screening and clinical diagnosis of diseased tissue. Fluorescence spectroscopy of intrinsic fluorophores has been studied to differentiate cancerous tissue from normal tissue since its first use in 1984 by Alfano [1]. Fluorescence spectroscopy can detect fluorophores at much lower concentration in tissue in comparison with absorption. Researchers can detect the fingerprints of main fluorophores such as: tryptophan, collagen, reduced nicotinamide adenine dinucleotide (NADH), and flavin adenine dinucleotide (FAD) etc. [2-5]. Human tissue is mainly composed of extracellular matrix of collagen fiber, proteins, fat, water, and epithelial cells. Tissues contain a number of key fingerprint endogenous fluorophore molecules: tryptophan, collagen, elastin, NADH, flavin and porohyrins. Tryptophan is an amino acid required by all forms of life for protein synthesis and other important metabolic functions [6], and is accounted as the major fluorophore contributing to protein in tissue. NADH and FAD can be used to probe changes in cellular metabolism [7]. The prim ary fluorophore in hu man tissue extracellular matrix (ECM) is type I collagen [8]. For invasion and subsequent metastasis, tumor cells degrade the surrounding collagen [8]. Conceivably the biochemical or morphologic changes that cause the spectral variations would appear earlier than the histological aberration [4]. Therefore, fluorescence holds a great promise as clinical tool for diagnosing early stage of carcinomas. To demonstrate the efficacy of the spectro scopic technique to distinguish the maligna nt tissue from the normal, a relative novel technique, namely Stokes Shift Spectroscopy (S3) was specially introduced for prostate and breast cancer detection. The S3 spectra of the key fluorophores in human breast tissue were analyzed using the Nonnegative Least Square (NNLS) method [9]. The linear discriminant analysis (LDA) was used to convert bio-molecular alterations reflected in the native spectra associated with process from the normal to cancer into valuable information. Subsequently, the receiver operating characteristic (ROC) curve was generated to evaluate the performance of the NNLS algorithm combined with LDA for diagnosis of human prostate/breast cancer.