Two different human stones, cystine and cholesterol from the kidney and gall bladder, were examined by time‐of‐flight secondary ion mass spectrometry using Ga+ primary ions as bombarding particles. The mass spectra of kidney stone were compared with those measured for the standard compounds, cystine and cysteine. Similar spectra were obtained for the stone and cystine. The most important identification was based on the existence of the protonated molecules [M + H]+ and deprotonated molecules [M‐H]‐. The presence of cystine salt was also revealed in the stone through the sodiated cystine [M + Na]+ and the associated fragments, which might be due to the patient treatment history. In the gallstone, the deprotonated molecules [M‐H]+ of cholesterol along with relatively intense characteristic fragments [M‐OH]+ were detected. Copyright © 2012 John Wiley & Sons, Ltd.