Despite several electrocardiographic, echocardiographic, electrophysiologic and pathologic studies, the cause of abnormal Q waves in patients with HCM remains unclear. Cardiovascular magnetic resonance (CMR) is a powerful in vivo diagnostic tool for evaluating cardiac morphology and function. We hypothesized that estimation of segmental and transmural extent of myocardial enhancement by late gadolinium enhancement (LGE) CMR could clarify the basis of Q waves. The purpose of this prospective study was to evaluate the morphological basis of abnormal Q waves in hypertrophic cardiomyopathy (HCM) as assessed by CMR. Thirty-eight patients with HCM underwent gadolinium-enhanced CMR and 12 lead electrocardiography (ECG). Left ventricular function, volumes, segmental and transmural extent of myocardial LGE were assessed and analysed in relation to the presence of abnormal Q waves. Twelve (31%) of the 38 patients had abnormal Q waves on the ECG. Patients with Q waves exhibited significantly more myocardial LGE segmentally as well as transmurally than patients without Q waves. As the segmental and the transmural extent of LGE increased, the probability of Q wave increased (anterior: segmental extent chi2 = 10, p = 0.0013, transmural extent chi2 = 10, p = 0.0013; inferior: segmental extent chi2 = 13, p = 0.0003, transmural extent chi2 = 15, P < 0.0001: lateral: segmental extent chi2 = 10, p = 0.0016, transmural extent chi2 = 10, p = 0.0012). Additionally, the ratio of septal to posterior wall thickness was significantly higher in patients with Q waves than in patients without Q waves (2.3 vs. 1.6, p = 0.012). It seems that segmental and transmural extent rather than the mere presence of myocardial LGE is the underlying mechanism of abnormal Q waves in HCM. Additionally, distribution of hypertrophy as indicated by differences in the ratio of septal to posterior wall thickness seems to play an important role.