Microvolt T-wave alternans (MTWA) is an electrocardiographic marker for predicting sudden cardiac death. In this study, we aimed to study the relation between MTWA and scar assessed with cardiac magnetic resonance imaging (CMR) in patients with ischemic cardiomyopathy (ICM) or dilated cardiomyopathy (DCM). Sixty-eight patients with positive or negative MTWA and analysable CMR examination were included. Using CMR and the delayed enhancement technique, left ventricular ejection fraction (LVEF), volumes, wall motion and scar characteristics were assessed. Overall, positive MTWA (n = 40) was related to male gender (p = 0.04), lower LVEF (p = 0.04) and increased left ventricular end-diastolic volume (LVEDV) (p < 0.01). After multivariate analysis, male gender (p = 0.01) and lower LVEF remained significant (p = 0.02). Scar characteristics (presence, transmurality, and scar score) were not related to MTWA (all p > 0.5). In the patients with ICM (n = 40) scar was detected in 38. Positive MTWA (n = 18) was related to higher LVEDV (p = 0.05). In patients with DCM (n = 28), scar was detected in 11. Trends were found between positive MTWA (n = 15) and male gender (p = 0.10), lower LVEF (p = 0.10), and higher LVEDV (p = 0.09). In both subgroups, the presence, transmurality or extent of scar was not related to MTWA (all p > 0.45). In this small study, neither in patients with ICM or DCM a relation was found between the occurrence of MTWA and the presence, transmurality or extent of myocardial scar. Overall there was a significant relation between heart failure remodeling parameters and positive MTWA.