The invention provides methods and compositions for determining whether a subject containing a stent immobilized in a blood vessel has asymptomatic stent thrombosis or is at risk of developing clinically symptomatic stent thrombosis. In one approach, the method involves imaging a region of the blood vessel that contains the stent using a probe that contains a fluorochrome, for example, a near-infrared fluorochrome, and a targeting moiety that binds a molecular marker indicative of the presence of asymptomatic stent thrombosis or the development of symptomatic stent thrombosis. To the extent that the subject displays one or more such markers, the probe binds to the markers and increases the local concentration of the probe in the vicinity of the stent. The imaging method identifies those patients that display a higher density of such markers in the vicinity of the stent. As a result, those patients can be monitored for, and/or treated to prevent, symptomatic stent thrombosis.