A medical retrieval device and method used in endoscopic procedures to retrieve stones has a shaft comprising a sheath with a lumen and a drive wire slidably disposed within the lumen for operating a stone entrapping mechanism on the distal end of the retrieval device. The shaft has an average outside diameter of less than 1.9 Fr. The shaft, sheath and drive wire each have proximal, intermediate and distal portions, and each of the corresponding portions are in generally similar locations along the longitudinal length of the device. The proximal portions of the shaft and the drive wire are preferably stiffer than the corresponding intermediate portions of the shaft and drive wire. The proximal and intermediate portions of the sheath have generally similar stiffnesses. The shaft reduces flow resistance within the working channel of an endoscope, increasing the flow of irrigation fluid in order to improve procedural visibility. The shaft varies in flexibility to match the requirements of a flexible endoscope and facilitate deflection of the endoscope.