Microstructural and biomolecular preservation is reported in fossils as old as the Triassic. Such preservation suggests unusual taphonomic conditions. We collected fragments of fossil whale bone from silty, tuffaceous, and diatomaceous rocks of the middle-upper Miocene portion of the Pisco Formation. The whale fossils within the region are generally well-preserved and mostly articulated, including some specimens with in situ baleen. Due to the depositional setting associated with the preservation of these fossils, they could be expected to be favorable candidates for the preservation of cellular microstructures and/or original biomolecules. To test this hypothesis, fossil whale bone fragments were subjected to microscopic analysis and EDTA-mediated demineralization to release extractable materials. Microscopy of partially demineralized fossil bones revealed quartz-permineralized osteocyte-like and vessel-like structures. Protein assay (micro-Bicinchoninic Acid Assay) of the supernatants obtained from demineralized fossils yielded 12 to 19.5 μg of protein per gram of bone. MALDI-TOF analysis of the extracted protein demonstrated the presence of approximately 5 kD molecules in one fossil sample, consistent with the presence of highly fragmented polypeptides. An LC-MS/MS analysis of the fragmentation pattern of the tryptic digest of extracted protein was performed. However, attempted protein identification was unsuccessful. Nevertheless, this study first documents the microstructural preservation with some silicification of the fossil whale bones of the Pisco Formation, and then quantifies extractable protein from these bones. It adds to the growing body of reports of microstructural and organic preservation in fossils.