While calcium oxalate monohydrate (whewellite: CaC₂O₄·H₂O) kidney stones are related to hyperoxaluria, calcium oxalate dihydrate (weddellite: CaC₂O₄·(2 + x)H₂O) ones are mainly associated with hypercalciuria. Crystalline conversion from weddellite to whewellite introduces a contradiction between Fourier transform infrared (FTIR) spectra which indicate the presence of whewellite and the fact that bipyramid crystallites, a morphology specific of weddellite, can be observed. It constitutes thus a major problem for clinicians as hyperoxaluria and hypercalciuria are associated with very different aetiologies and treatments. In this contribution, the complete set of data including neutron diffraction experiments, observations through a last generation field emission scanning electron microscope as well as 3D and 2D cross-section visualisations derived from the μComputed Tomography measurements seems to explain some particular features observed on FTIR spectra related to the crystalline conversion from weddellite to whewellite. The structural hypothesis which is proposed is related to the formation of amorphous whewellite, a new polymorph recently synthesised. Thus, in such cases, special attention should be paid to the stone morphology (and not FTIR spectrum), which is a major element for clinical diagnosis as already underlined for other types of urinary calculi.