A fatty liver is known to have impairment of microcirculation, which is worsened after ischemia reperfusion injury (IRI). This makes most fatty grafts unsuitable for transplantation, and in the absence of real time assessment of microcirculation this selection has been at best, random. The goal of this study was to demonstrate the utility of a contrast enhanced ultrasound model in quantitative assessment of the microcirculation of a fatty liver. We subjected fatty mice to IRI and blood flow dynamics were assessed before and after the injury. There was a significant increase in the resistive and pulsatility index of the extra hepatic artery and a significant decrease in velocity of the portal vein. There was also a quantifiable decrease in the intrahepatic blood volume, blood flow, time to peak flow, and perfusion index of mice with fatty liver suggesting that a fatty liver develops hemodynamic abnormalities after IRI, leading to increased hepatocellular injury. Importantly, these abnormalities can be reliably quantified by using a contrast, enhanced Doppler ultrasound, an inexpensive technique with multiple clinical applications. It can be used to assess the quality of the fatty liver donor graft prior to organ retrieval; for determining live donor candidacy, for making post IRI recovery prognosis, and for assessing the effectiveness of therapeutic interventions.