Calcium carbonate and carbonate-hydroxyapatite are known to form inorganic components of crystals and calcareous concretions found in many non-skeletal tissues and structures including the pineal gland. We used advanced surface analyses techniques such as polarization microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), microfocus X-ray diffraction (XRD), transmission electron microscopy with selected area electron diffraction (TEM-SAED) to investigate samples extracted from rat pineal gland after irradiation with visible light for 12 h. Single-crystal X-ray diffraction showed that the concretions were largely amorphous with the presence of some nanocrystalline phases. High resolution TEM-SAED revealed the presence of iron oxide in the form of hematite. Spectroscopy data especially Raman spectroscopy revealed a mixed nature of these concretions, which corresponded reasonably with XPS, TEM and XRD. Overall the study confirms the presence of a mixed phase of calcium carbonates including calcite, aragonite and vaterite. We note that aragonite is not a common occurrence in vertebrates and recommend further investigation to rule out any link to pathology.