Rapid Doppler shifts highlight some kidney stones with a rapid change in color in ultrasound imaging which is called the “twinkling artifact.” Many hypotheses exist to describe the mechanism of twinkling, including the hypothesis that microbubbles are stabilized in crevices on the surface of kidney stones. The objective is to evaluate the distribution of stable microbubbles on kidney stone surfaces with humidity-controlled scanning electron microscopy (ESEM) and determine whether any sub-surface characteristics as assessed with micro-computed tomography (µCT) may contribute to twinkling. A Verasonics® research ultrasound system with the Verasonics L22-14 and Philips/ATL L7-4 and C5-2 transducers quantified twinkling. Results show a correlation between voids within kidney stones and the locations of twinkling on the stone surface. These voids had a calculated free-field Minneart resonant frequency of 3–9 MHz depending on the size. ESEM revealed that surfaces that twinkled had more crevices with radii corresponding to bubbles with a free-field resonant frequency of 3–7 MHz. These results suggest that internal voids and surface crevices contribute to the twinkling artifact on kidney stones.