The arterial structure cyclically fluctuates in three-dimensions (3-D) caused by pulsatile blood flow. The evaluation of arterial wall motion and hemodynamics contributes to early diagnosis of carotid atherosclerosis. Ultrasound is one of the most appropriate imaging modalities to evaluate arterial wall motion in real time. Although many previous studies have discussed the mechanical properties of the carotid artery bifurcation (CAB) from the two-dimensional (2-D) view, the spatio-temporal variation of carotid artery geometry in 3-D has not yet been investigated in detail. In this study, the 3-D data set of CAB from rats was acquired using a high spatio-temporal resolution ultrasound imaging system with a 40 MHz probe using mechanical sector scanning. A total of 31 slices of cross-section images were stored and a spoke scan algorithm was implemented to radially scan the lumen area in polar coordinates based on a pre-tracked seed point. The boundary of the arterial lumen was segmented using intensity-threshold-based boundary detection and fitted by polynomial regression. Two operators, who were trained with the same protocol to minimize inter- and intra-operator variability, manually segmented the lumen boundary on systolic and diastolic phase from the gray-scale images. Finally, the 3-D lumen geometries of CAB during one cardiac cycle were constructed based on the segmented lumen boundaries. From this constructed 3-D geometry, we observed that the CAB geometry favorably expanded to the anterior/posterior direction, parallel to the sagittal plane; and the manually segmented geometry also confirmed the asymmetrical change in bifurcation geometry. This is the first study on visualization and quantification on the asymmetrical variation of the CAB geometry of a rat in 3-D during a whole cardiac cycle. This finding may be useful in understanding hemodynamic etiology of various cardiovascular diseases such as arterial stenosis and its complications, and also provides reference information for numerical simulation studies on arterial wall motion.