OBJECTIVE Bacterial imprints are always observed on highly carbonated apatite kidney stones but not struvite kidney stones. Struvite and carbonated apatite stones with a high CO32–/PO43– rate are believed to develop from infections, but their structural differences at the mesoscopic scale lack explanation. METHODS We investigated 17 urinary calculi composed mainly of struvite or carbonated apatite by Fouriertransform infrared, scanning electron microscopy, and powder neutron diffraction techniques. RESULTS Carbonated apatite but not struvite stones showed bacterial imprints. If the same stone contained both carbonated apatite and struvite components, bacterial imprints were observed on the carbonated apatite but not the struvite part. Moreover, neutron powder diffraction experiments revealed the crystal size of struvite stones were larger than that of carbonated apatite stones (250 50 vs 50 nm). CONCLUSION Bacterial imprints may appear more easily on kidney stones with small nanocrystals, such as carbonated apatite than with large nanocrystals, such as struvite. This approach may help identify