The influence of different solvents on cholesterol and pigment stones was investigated in vitro. Stone analysis was performed chemically, with infrared spectroscopy (IRS), scanning electron microscopy, energy-dispersive X-microanalysis (EDXA) and wave-length-dispersive X-microanalysis (WDXA). Each set of stones came from one source: eight human calcified cholesterol stones (CHS), eight fragments of bovine radiopaque Ca-bilirubinate stones (BBIL), and two complete BBIL. CHS and BBIL fragments were treated with (1) a buffered, alkaline 1% ethylenediamine tetraacetate solution (BA-EDTA; pH 9.5); (2) with BA-EDTA and monooctanoin preparation (GMOC) alternately; (3) with GMOC alone, and (4) with methyl-tert-butyl ether (MTBE). The complete BBIL were treated with BA-EDTA and MTBE. Furthermore, two human black pigment stones (BPS) were incubated in BA-EDTA. Calcified cholesterol stones are not dissolved by GMOC alone, nor by alternating treatment with BA-EDTA. They are dissolved by MTBE. MTBE is unsuitable for complete Ca-bilirubinate stones but MTBE, GMOC and GMOC/BA-EDTA alternately disaggregate stone fragments. This means that stone fragments behave differently from complete Ca-bilirubinate stones, which is important for further in vitro investigations. Ca-bilirubinate and black pigment stones are disaggregated in BA-EDTA. These results were confirmed with six CHS, 12 BBIL and 12 BPS from 5 further patients, incubated in the most eligible solvent for any individual stone type.