Cardiologists use two-dimensional projection images in conventional X-ray coronary angiography for the assessment of three-dimensional structures. During minimally invasive interventions there is a need to clearly visualize and analyze contrast filled coronary arteries, surrounding tissue, and implanted devices. Three-dimensional reconstruction of these structures is challenging due to the cardiac and respiratory motion. In this paper we describe a method to automatically generate motion compensated reconstructions of various structures using rotational X-ray angiography. The method uses markers on a device or guide wire to identify and estimate the motion of an object or region of interest in order to register and motion compensate the projection images to generate a motion compensated reconstruction. The method is evaluated on 20 rotational acquisitions and the average marker couple detection rate is 84% for cardiac stents, 90% for closure devices and 20% for contrast filled coronaries. The projection images are motion compensated based on the semi-automatically detected markers and subsequently used for reconstruction. We conclude that it is feasible to reconstruct cardiac stents, closure devices, contrast filled coronaries, and calcified plaques using rotational X-ray angiography.