A mitral L-wave indicates advanced diastolic dysfunction with elevated left ventricular filling pressure. Previous studies have reported that the presence of a mitral L-wave is associated with a poor prognosis in patients with heart failure. However, whether the L-wave can predict adverse events in patients with hypertrophic cardiomyopathy (HC) is still unclear. Therefore, we aimed to investigate the prevalence of a mitral L-wave in patients with HC, and the prognosis of patients with or without an L-wave. We analyzed 445 patients with HC. The end points of this study were HC-related death, such as sudden death or potentially lethal arrhythmic events, heart failure-related death, and stroke-related death. A mitral L-wave was defined as a distinct mid-diastolic flow velocity after the E wave with a peak velocity >20 cm/s. The prevalence of an L-wave was 32.4% in patients with HC. Patients with an L-wave were significantly younger, more likely to be women, had higher New York Heart Association functional class, and had a higher prevalence of atrial fibrillation than did patients without an L-wave. Patients with an L-wave had a significantly higher incidence of HC-related death compared with those without an L-wave (log-rank, p < 0.001). The L-wave was an independent determinant of HC-related death in multivariate analysis adjusted for imbalanced baseline variables (adjusted hazard ratio 2.38; 95% confidence interval 1.42 to 4.01; p = 0.001). In conclusion, the presence of a mitral L-wave may be associated with adverse outcome in patients with HC.