Stem cell transplantation is one of the attractive therapeutic strategies for the treatment of hindlimb ischemia. However, few studies have quantitatively assessed perfusion noninvasively in deep tissues after cell transplantation. In this study, we examined the feasibility of contrast sonography for the assessment of perfusion after bone marrow-derived mesenchymal stem cell (MSC) transplantation by using a rat unilateral hindlimb ischemia model. The quantitative parameters derived from contrast sonography were compared with the colored microspheres-derived blood flow and the capillary density. Nine rats were assigned each to a control (saline injection) or a treated (MSC transplantation) group. Video intensity vs. pulsing interval plots were acquired with ultraharmonic imaging of SONOS5500 during IV infusion of Levovist. The left-to-right ratio of hindlimb blood volume (A-ratio), microbubble velocity (beta-ratio) and hindlimb blood flow (Abeta-ratio) were calculated. The MS-ratio, the ratio of the left to the right hindlimb blood flow determined using colored microspheres, was also calculated. Although A-ratio did not change, beta- and Abeta-ratio in the treated group were significantly higher than those in the control group. In addition, MS-ratio and capillary density in the treated group were significantly higher than those in the control group. Compared with A- and Abeta-ratio, beta-ratio had the highest correlation with MS-ratio and capillary density (vs. MS-ratio: r = 0.66, p < 0.01; vs. capillary density: r = 0.52, p < 0.05). The results of our study imply that the contrast sonography-derived beta-ratio is a useful parameter that reflects the perfusion after cell transplantation in ischemic hindlimb.