A system and method for determining a disease state and clinical outcome of a sample. A sample is illuminated to produce Raman scattered photons, the Raman scattered photons are assessed to generate a Raman spectroscopic data set representative of the sample, wherein said Raman spectroscopic data set comprises at least one of: a Raman spectra of the sample and a spatially accurate wavelength resolved Raman image of the sample; the Raman spectroscopic data set is evaluated using a chemometric technique to classify the disease state of the sample as: acute, chronic, incipient, or none. In one embodiment, the chemontric technique is principle component analysis. In another embodiment, the sample is obtained prior to transplantation and analysis can determine the likelihood of rejection by a host.