In this work, we show that molecularly-sensitive contrast can be generated in OCT using targeted multifunctional magnetic microspheres. These microspheres were engineered to target the ΑvΒ3 integrin for the localization of atherosclerotic lesions in excised aortas from a rabbit animal model. The aortas were extracted and placed in a flow chamber, which mimicked the physiological blood flow conditions in the living rabbit. Magnetic microspheres were perfused through the aorta inside the flow chamber and catheter-based OCT imaging, magnetomotive optical coherence tomography (MM-OCT), fluorescence confocal, and bright field microscopy was performed on the ex vivo aorta specimens for localizing the microspheres. Results showed successful targeting of the functionalized microspheres to early atherosclerotic lesions, and good co-registration of MM-OCT signal with confocal microscopy.