This study introduces a 3D whole-heart sequence with image-based navigation for non-contrast enhanced coronary lumen and coronary thrombus/haemorrhage characterization. The sequence is based on a phase sensitive inversion recovery (PSIR)-like approach enabling the acquisition of two bright-blood datasets for visualization of the coronary lumen and estimation of motion parameters. Furthermore, a third, fully co-registered dark-blood dataset for thrombus/haemorrhage characterization is obtained from the PSIR reconstruction. With the proposed approach the coronary lumen is visualized with improved SNR/CNR and vessel sharpness when compared to a conventional T2 prepared coronary MRA acquisition. In addition, effective blood signal suppression and feasibility for thrombus visualization is shown with the PSIR reconstructed black-blood dataset.