Fluorescence spectroscopy contains diagnostic information about the lung biochemistry and morphology, including tissue optical properties and fluorophores. However, the fluorophore information is generally masked by the optical properties of the tissue, which complicates the evaluation of their role in lung-cancer detection. In this work, we have developed a method for extracting the intrinsic fluorescence spectra from the endoscopic measurements of the combined fluorescence and reflectance spectra. Principle components and classification analysis was performed to evaluate the diagnostic potential of the extracted intrinsic fluorescence spectra from in vivo combined fluorescence and reflectance spectral measurements. We evaluated the diagnostic sensitivity and specificity of both the intrinsic fluorescence and the fluorescence spectra. The results showed that the intrinsic fluorescence spectra contain significant diagnostic information that had been masked by the lung optical properties. We have also found that the intrinsic fluorescence has improved the specificity for endobronchial-cancer detection, although with a slight decrease in the detection sensitivity, when compared to the fluorescence spectra. This may indicate that intrinsic fluorescence analysis could be used to improve the diagnostic specificity of fluorescence spectroscopy and imaging.