Wire-induced denudation of carotid arteries in apolipoprotein-E deficient mice has been well established as a model to study the spontaneous development of atherosclerotic lesions and neointima formation after injury. In general, such models are evaluated by ex vivo histopathology providing information on vessel morphology and stenosis at the time of harvest only. Consequently, fast, non-invasive 3D monitoring of arteries would be highly desirable for the continuous analysis of neointima formation in mice. In the present study we have established fast 2D and 3D MR methods for in vivo monitoring of carotid artery morphology at different time points after injury. 3D data were segmented using self-developed software (AngioTux). MR data showed excellent agreement to morphometric data obtained in two positions 4 weeks after injury (3D vs. Hist.: R²=0.964 and 0.986; 2D vs. Hist.: R²=0.974 and 0.970). Furthermore, monitoring of individual mice enabled us to detect different courses of vascular remodeling depending on the degree of injury. Quantification of luminal areas and volumes led to highly reproducible results with low intra- and interobserver variabilities. In conclusion, we describe high resolution 2D and 3D MRI techniques suitable to sensitively measure the extent and time course of changes in vessel morphology in mice in a repetitive manner. 3D data sets of excellent quality can be acquired within only 4 minutes and quantification is highly reproducible.