Scanning electron microscopy with or without conventional energy dispersive x-ray microanalysis is currently used to identify gallstone microstructure and inorganic composition. Organic calcium salts are among many biliary constituents thought to have a role in gallstone nidation and growth. However, current analytical techniques which identify these salts are destructive and compromise gallstone microstructural data. We have developed a new technique for gallstone analysis which provides simultaneous structural and compositional identification of calcium salts within gallstones. Backscattered electron imaging is used to localize calcium within cholesterol at minimum concentrations of 0.01%. Windowless energy dispersive x-ray microanalysis produces elemental spectra of gallstone calcium salts which are qualitatively and quantitatively different. These combined techniques provide simultaneous structural and compositional information obtained from intact gallstone cross-sections and have been used to identify calcium salts in gallstones obtained at cholecystectomy from 106 patients.