Background: The aim of this study was to investigate the potential impact of performing two-dimensional echocardiography (2DE) compared to cardiovascular magnetic resonance (CMR) for left ventricular ejection fraction (LVEF) on implantable cardioverter defibrillator (ICD) eligibility. Methods: A prospective cohort of 166 consecutive patients with nonischemic cardiomyopathy (NICM) was designed to compare transthoracic 2DE and CMR imaging. Results: Echocardiography measurements have important differences and large limits of agreement compared to CMR, especially when assessing ventricle volumes, and smaller but relevant differences when assessing LVEF. The agreement between CMR and 2DE regarding the identification of subjects with EF <= 35, respectively <= 30, and thus eligible for an ICD measured by Cohen’s Kappa was 0.78 (95% CI: 0.68–0.88), p < 0.001, respectively 0.65 (95% CI: 0.52–0.78), p < 0.001. The disagreement represented 7.9%/11.3% of the subjects who had EF < 35%/< 30% as observed by CMR, who would have been classified as eligible for an ICD, resulting in an additional need to use an ICD. Moreover, 2.6%/3.3% would have been deemed eligible by echocardiography for an ICD. Conclusions: These measurement problems result in incorrect assignments of eligibility that may have serious implications on the quality of life and the prevention of death events for patients assessed for eligibility of an ICD.