<b><i>Objectives:</i></b> The clinical outcomes of hypertrophic cardiomyopathy (HCM) are largely unpredictable. This study aimed to investigate the relationship between atrial fibrillation (AF) and its prognostic implications in Chinese patients with HCM. <b><i>Methods:</i></b> From 1999 to 2011, 654 unrelated HCM patients were consecutively recruited at Fuwai Hospital. Medical history, including electrocardiographic and echocardiographic data, was analyzed. <b><i>Results:</i></b> AF was documented in 158 patients (24%). During follow-up of 4.2 ± 2.8 years, Kaplan-Meier analysis revealed that the presence of AF was associated with an increased risk for all-cause death (p = 0.001), cardiovascular death (p < 0.001), severe heart failure (p < 0.001) and ischemic stroke (p < 0.001). Multivariate analysis identified AF as an independent predictor of stroke-related death (HR 6.71, 95% CI 1.23-38.58, p = 0.03), advanced heart failure (HR 1.83, 95% CI 1.04-3.22, p = 0.04) and ischemic stroke (HR 9.98, 95% CI 4.06-24.53, p < 0.001). Furthermore, enlarged left atrial diameter was positively related to all-cause death (HR 1.09, 95% CI 1.05-1.13, p < 0.001), cardiovascular death (HR 1.08, 95% CI 1.04-1.20, p < 0.001) and development of advanced heart failure (HR 1.05, 95% CI 1.01-1.10, p = 0.01). <b><i>Conclusions:</i></b> AF predicts poor outcomes for patients with HCM. Left atrial dilation is also related to an adverse prognosis and provides additional prognostic information
