Multispectral fluorescence imaging (MSFI) is a powerful imaging modality for tissue analysis and diagnostic imaging. By illuminating with distinct wavelengths of light, intrinsic biological fluorophores and labeled markers can be measured, providing information about tissue metabolism and function. MSFI has shown promise in the scope of gastrointestinal (GI) cancers such as colon and gastric cancers. Before MSFI can be used as an endoscopic diagnostic tool there requires extensive characterization of tissue properties to identify biomarker variations that occur with the onset of disease. A robust, whole organ imaging instrument to characterize autofluorescence properties would greatly inform the development of diagnostic imaging platforms. This paper reviews the design and validation of a multispectral fluorescence imaging system for characterizing whole organ tissue fluorescence and reflectance properties. We present a detailed discussion on design considerations and demonstrate excellent performance suitable to detect tissue autofluorescence.