To compare three-dimensional (3D) whole-heart MRI with isotropic submillimeter resolution with standard two-dimensional (2D) cine MRI in measuring the bilayered myocardium in left ventricular noncompaction (LVNC). Twenty-four patients with LVNC (mean age, 42 years ± 16 [SD]) were retrospectively enrolled between October 2011 and July 2020. Compacted myocardium (CM) and noncompacted myocardium (NCM) were measured in long axis (Petersen approach) and short axis (Jacquier approach) at 3D whole-heart and 2D cine MRI by two independent readers. Image quality (1 = excellent, 2 = adequate, 3 = nondiagnostic), considering discrimination between NCM and CM and CM and adjacent tissue, was evaluated. Pearson, Spearman, and intraclass correlation tests were used as statistical tests. In long-axis measurements, the correlation between both sequences was moderate to strong for CM (Pearson, 0.66-0.79; Spearman, 0.61-0.68) and strong to very strong for NCM (Pearson, 0.90-0.97; Spearman, 0.77-0.91). Intraclass correlation coefficient (ICC) in 3D whole-heart MRI was 0.90 (95% CI: 0.78, 0.95) for CM and 0.94 (95% CI: 0.84, 0.97) for NCM, while ICC in 2D cine MRI was 0.77 (95% CI: 0.55, 0.89) for CM and 0.87 (95% CI: 0.72, 0.94) for NCM. Short-axis CM and NCM measurements had a strong to very strong correlation between both sequences (Pearson, 0.86-0.98; Spearman, 0.82-0.98). ICC in 3D whole-heart MRI was 0.96 (95% CI: 0.94, 0.99) for CM and 0.98 (95% CI: 0.97, 0.99) for NCM, while ICC in 2D cine MRI was 0.82 (95% CI: 0.63, 0.92) for CM and 0.87 (95% CI: 0.72, 0.94) for NCM. 3D whole-heart MRI demonstrated higher image quality than did 2D cine MRI (P < .001). 3D whole-heart MRI revealed higher image quality, with better structure discrimination and interobserver agreement in LVNC measurements, compared with standard 2D cine images.Keywords: MR Imaging, Cardiac, Cardiovascular Magnetic Resonance, Left Ventricular Noncompaction, Free-breathing Imaging Technique Supplemental material is available for this article. © RSNA, 2022See also the commentary by Jensen and Petersen in this issue.