Decellularization of tissues and organs is a successful platform technology for creating scaffolding materials for tissue engineering and regenerative medicine. It has been suggested that the success of these materials upon implantation is due to the molecular signals provided by the remaining scaffold extracellular matrix (ECM) components presented to probing cells in vivo as they repopulate the surface. For this study, decellularized matrices were created from esophagus, bladder, and small intestine harvested from adult male Fischer 344 rats. The three decellularized matrices (each originating from source tissues which included an epithelial lining on their luminal surfaces) were immunostained for collagen IV and laminin to determine basement membrane retention. Scanning electron micrographs of the surfaces were used to provide insight into the surface topography of each of the decellularized tissues. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to generate high-resolution mass spectra for the surfaces of each scaffold. This surface-sensitive technique allows for detailed molecular analysis of the outermost 1-2 nm of a material and has been applied previously to thin protein films and secreted ECM proteins on poly(N-isopropyl acrylamide) (polyNIPAAM) surfaces. To extract trends from within the complex ToF-SIMS dataset, a multivariate analysis technique, principal component analysis (PCA), was employed. Using this method, a molecular fingerprint of each surface was created and separation was seen in the PCA scores between the decellularized esophagus and the decellularized small intestine samples. The PCA scores for the decellularized bladder sample fell between the previous two decellularized samples. Protein films of common extracellular matrix constituents (collagen IV, collagen I, laminin, and Matrigel) were also investigated. The PCA results from these protein films were used to develop qualitative hypotheses for the relationship of the key fragments identified from the PCA of the decellularized ECMs.