Techniques are provided for detecting and distinguishing stroke and cardiac ischemia within a patient using an implantable medical device. In one example, a preliminary indication of stroke is detected by a pacemaker or similar implantable device based on an analysis of features of an intracardiac electrogram (IEGM) sensed by the device. Exemplary IEGM features indicative of possible stroke include the onset of prominent U-waves, the onset of notched T-waves, and changes in ST segment duration or QT duration. Upon detection of a possible stroke, the device then detects one or more hemodynamic parameters that are typically affected by cardiac ischemia. Such hemodynamic parameters can include, e.g., cardiac contractility or stroke volume. The device then distinguishes stroke and cardiac ischemia from one another based on whether any changes detected in the hemodynamic parameters are consistent with cardiac ischemia. Implantable systems that exploit subcutaneous electrocardiograms (ECGs) rather than IEGMs are also described.