PurposeTo develop a free‐running (free‐breathing, retrospective cardiac gating) 3D myocardial T1 mapping with isotropic spatial resolution.MethodsThe free‐running sequence is inversion recovery (IR)‐prepared followed by continuous 3D golden angle radial data acquisition. 1D respiratory motion signal is extracted from the k‐space center of all spokes and used to bin the k‐space data into different respiratory states, enabling estimation and correction of 3D translational respiratory motion, whereas cardiac motion is recorded using electrocardiography and synchronized with data acquisition. 3D translational respiratory motion compensated T1 maps at diastole and systole were generated with 1.5 mm isotropic spatial resolution with low‐rank inversion and high‐dimensionality patch‐based undersampled reconstruction. The technique was validated against conventional methods in phantom and 9 healthy subjects.ResultsPhantom results demonstrated good agreement (R2 = 0.99) of T1 estimation with reference method. Homogeneous systolic and diastolic 3D T1 maps were reconstructed from the proposed technique. Diastolic septal T1 estimated with the proposed method (1140 ± 36 ms) was comparable to the saturation recovery single‐shot acquisition (SASHA) sequence (1153 ± 49 ms), but was higher than the modified Look‐Locker inversion recovery (MOLLI) sequence (1037 ± 33 ms). Precision of the proposed method (42 ± 8 ms) was comparable to MOLLI (41 ± 7 ms) and improved with respect to SASHA (87 ± 19 ms).ConclusionsThe proposed free‐running whole heart T1 mapping method allows for reconstruction of isotropic resolution 3D T1 maps at different cardiac phases, serving as a promising tool for whole heart myocardial tissue characterization.