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Abstract Background Dual-phase 3-dimensional whole-heart acquisition allows simultaneous imaging during systole and diastole. Respiratory navigator gating and tracking of the diaphragm is used with limited accuracy. Prolonged scan time is common, and navigation often fails in patients with erratic breathing. Image-navigation (iNAV) tracks movement of the heart itself and is feasible in single phase whole heart imaging. To evaluate its diagnostic ability in congenital heart disease, we sought to apply iNAV to dual-phase sequencing. Methods Healthy volunteers and patients with congenital heart disease underwent dual-phase imaging using the conventional diaphragmatic-navigation (dNAV) and iNAV. Acquisition time was recorded and image quality assessed. Sharpness and length of the right coronary (RCA), left anterior descending (LAD), and circumflex (LCx) arteries were measured in both cardiac phases for both approaches. Qualitative and quantitative analyses were performed in a blinded and randomized fashion. Results In volunteers, there was no significant difference in vessel sharpness between approaches (p > 0.05). In patients, analysis showed equal vessel sharpness for LAD and RCA (p > 0.05). LCx sharpness was greater with dNAV (p