This project sought to test the ability of commercial stone analysis laboratories to correctly analyze urinary stones. Human stone specimens were cleaved into pieces, and the pieces of each specimen were verified as being similar using micro-computed tomography (micro CT), a non-destructive method. Thus, similar specimens from 25 stones were sent to five laboratories, and a sixth piece was kept for analysis in our laboratory using Fourier-transform infrared spectroscopy (FT-IR). The results showed that laboratories were very good at analyzing pure specimens, but with mixed specimens the accuracy and consistency varied. In six stones containing apatite, a mineral easily identified using micro CT, apatite was missed 20% of the time. Struvite content in the specimens was inconsistently reported, with laboratories differing in their reports of the presence of struvite in six of the 25 stones (24%). A mixed stone containing atazanavir was not reported by any of the laboratories as containing that drug. Nomenclature differed among the laboratories, especially with regard to apatite, which was variously reported as hydroxyapatite, carbonate apatite, or as apatite with calcium carbonate. One laboratory reported protein in every stone, while for all others protein was reported in only one stone. We conclude that physicians need to be aware that reports on mixed stones, which represent >90% of all calculi, can be erroneous. It is likely that supplying a greater amount of stone material will assist a laboratory in making a correct analysis of mixed stones. Also, standardization of nomenclature could assist in analysis reproducibility, but this remains to be tested.