Multifocal cerebrovascular gas embolism occurs frequently during cardiopulmonary bypass and is thought to cause postoperative neurological dysfunction in large numbers of patients. We developed a mathematical model to predict the absorption time of intravascular gas embolism, accounting for the bubble geometry observed in vivo. We modeled bubbles as cylinders with hemispherical end caps and solved the resulting governing gas transport equations numerically. We validated the model using data obtained from video-microscopy measurements of bubbles in the intact cremaster microcirculation of anesthetized male Wistar rats. The theoretical model with the use of in vivo geometry closely predicted actual absorption times for experimental intravascular gas embolisms and was more accurate than a model based on spherical shape. We computed absorption times for cerebrovascular gas embolism assuming a range of bubble geometries, initial volumes, and parameters relevant to brain blood flow. Results of the simulations demonstrated absorption time maxima and minima based on initial geometry, with several configurations taking as much as 50% longer to be absorbed than would a comparable spherical bubble.