Optimization of contrast-enhanced imaging and focused ultrasound therapy requires a comprehensive understanding of in vivo microbubble (MB) pharmacokinetics. Prior studies have focused pharmacokinetic analysis on indirect techniques, such as ultrasound imaging of the blood pool and gas chromatography of exhaled gases. The goal of this work was to measure the MB concentration directly in blood and correlate the pharmacokinetic parameters with the MB size and dose. MB volume dose (MVD) was chosen to combine the size distribution and number into a single-dose parameter. Different MB sizes (2, 3, and 5 μm diameter) at 5-40 μL/kg MVD were intravenously injected. Blood samples were withdrawn at different times (1-10 min) and analyzed by image processing. We found that for an MVD threshold < 40 μL/kg for 2 and 3 μm and <10 μL/kg for 5 μm, MB clearance followed first-order kinetics. When matching MVD, MBs of different sizes had comparable half-lives, indicating that gas dissolution and elimination by the lungs are the primary mechanisms for elimination. Above the MVD threshold, MB clearance followed biexponential kinetics, suggesting a second elimination mechanism mediated by organ retention, possibly in the lung, liver, and spleen. In conclusion, we present the first direct MB pharmacokinetic study, demonstrate the utility of MVD as a unified dose metric, and provide insights into the mechanisms of MB clearance from circulation.