Vaterite and aragonite polymorphs in freshwater cultured pearls from mussels of the genus Hyriopsis (Unionidae) were structurally and compositionally characterized by Raman spectroscopy, Micro computer tomography, high resolution field emission scanning electron microscopy, electron microprobe analysis and laser ablation inductively coupled plasma mass spectrometry. The appearance of vaterite in pearls is related to the initial stages of biomineralization, although we demonstrate that vaterite can not be a precursor to aragonite. It is not related to a particular crystal habit and therefore does not have a structural functionality in the pearls. Larger contents of elements typically bound to organic molecules, such as P and S in vaterite, as well as larger total organic contents in vaterite as opposed to aragonite in conjunction with larger concentrations of Mn2+ and Mg2+, imply a stabilizing role of organic macromolecules and X
2+ ions for biological vaterite. Distribution coefficients between aragonite and vaterite for provenance-independent elements, such as Mn and Mg (0.27 and 0.04, respectively) agree very well with those observed in fish otoliths.