This paper highlights new research on the biomineralization of otoliths and uses a mineralogical approach to understand mechanisms of crystal growth and metal incorporation into otoliths. Petrographic observations of the nucleation of otolith growth in the core for several fish species reveals that sagittal otoliths appear to nucleate around a few or many nucleation sites (primordia) and that these sites vary in size (ranging in diameter from 1 to 20 μm), depending on the species. Spectroscopic data show a large Mn-enrichment in the primordia within the core but the reasons for this enrichment are still unclear (e.g. organic matter or possibly another material other than CaCO3). This study also provides the first multi trace-element data for endolymph fluid and the growing otolith; we found large enrichments (Ca and Sr) and depletions (Na, K, Zn and Rb) of elements in the otolith relative to the endolymph. The last part of this paper examines the effect of crystal structure on the microchemistry of otoliths. Our investigation helps understand how the chemical characteristics of the metal ions (i.e. ionic radii) and the crystalline structure interact to cause differential trace-metal uptake between the CaCO3 polymorphs, aragonite and vaterite.