Optical spectroscopy can be used to distinguish between healthy and diseased tissue. In this study, the design and testing of a single-pixel hyperspectral imaging (HSI) system that uses autofluorescence emission from collagen (400 nm) and nicotinamide adenine dinucleotide phosphate (475 nm) along with differences in the optical reflectance spectra to differentiate between healthy and thermally damaged tissue is discussed. The changes in protein autofluorescence and reflectance due to thermal damage are studied in ex vivo porcine tissue models. Thermal lesions were created in porcine skin (n=12) and liver (n=15) samples using an IR laser. The damaged regions were clearly visible in the hyperspectral images. Sizes of the thermally damaged regions as measured via HSI are compared to sizes of these regions as measured in white-light images and via physical measurement. Good agreement between the sizes measured in the hyperspectral images, white-light imaging, and physical measurements were found. The HSI system can differentiate between healthy and damaged tissue. Possible applications of this imaging system include determination of tumor margins during surgery/biopsy and cancer diagnosis and staging.