To evaluate the diagnostic accuracy of a prototype noncontrast, free-breathing, self-navigated 3D (SN3D) MR angiography (MRA) technique for the assessment of coronary artery anatomy in children with known or suspected coronary anomalies, using CT angiography (CTA) as the reference standard. Twenty-one children (15 male, 12.3 ± 2.6 years) were prospectively enrolled between July 2014 and August 2016 in this IRB-approved, HIPAA-compliant study. Patients underwent same-day unenhanced SN3D-MRA and contrast-enhanced CTA. Two observers rated the visualization of coronary artery segments and diagnostic confidence on a 3-point scale and assessed coronary arteries for anomalous origin, as well as interarterial and intramural course. Sensitivity, specificity, positive (PPV) and negative predictive values (NPV) of SN3D-MRA for the detection of coronary artery abnormalities were calculated. Interobserver agreement was assessed using Intraclass Correlation Coefficients (ICC). Fourteen children showed coronary artery abnormalities on CTA. The visualization of coronary segments was rated significantly higher for CTA compared to MRA (p <0.015), except for the left main coronary artery (p = 0.301), with good to excellent interobserver agreement (ICC = 0.62-0.94). Diagnostic confidence was higher for CTA (p = 0.046). Sensitivity, specificity, PPV, and NPV of MRA were 92%, 92%, 96%, and 87% for the detection of coronary artery anomalies, 85%, 85%, 74%, and 92% for high origin, 71%, 92%, 82%, and 87% for interarterial, and 41%, 96%, 87%, and 80% for intramural course. Noncontrast SN3D-MRA is highly accurate for the detection of coronary artery anomalies in pediatric patients while diagnostic confidence and coronary artery visualization remain superior with CTA.