Objective To investigate the gender difference of long term prognosis of patients with diastolic heart failure. Methods A total of 562 patients with diastolic heart failure were consecutively enrolled and 297 (52.8%) of them were female. The average follow-up time was 3.7 years. The primary end point was all-cause mortality. Cox regression analysis was adopted to investigate the gender difference of long term prognosis of patients with diastolic heart failure. Results Compared with male patients, female patients were older with higher systolic blood pressure and higher incidences of diabetes and anemia, but less smokers. The echocardiography examination showed that the end-diastolic volume and end-systolic volume of females were lower. The laboratory examination indicated that levels of total cholesterol, lower density lipoprotein, higher density lipoprotein and serum sodium of females were higher, while the red blood cell count and levels of hemoglobin, pre-albumin, alanine aminotransferase, serum creatinine, uric acid, urea nitrogen, serum potassium, cardiac troponin Ⅰ, and creatine kinase MB were lower. The differences of medications between males and females after hospital discharge were not statistically significant. During the follow-up, the all-cause mortality of all patients, female patients, and male patients were 24.0%, 23.9%, and 24.2%, respectively. Kaplan-Meier survival analysis (Log Rank, P=0.924), Cox univariate regression analysis (HR=1.016, 95%CI=0.725-1.425, P=0.924), and multivariate regression analysis (OR=0.922, 95%CI=0.571-1.490, P=0.741) after all clinical factors were corrected indicated that the long term survival rate of males was not significantly different from that of females. Cox univariate regression analysis of different genders showed that predictive factors of the elevated all-cause mortality of males were higher age, higher NYHA status, higher heart rate on admission, higher B-type natriuretic peptide, lower serum sodium, lower hemoglobin, lower albumin, renal insufficiency, and higher uric acid. Predictive factors of the elevated all-cause mortality of females were higher age, higher NYHA status, higher heart rate on admission, higher B-type natriuretic peptide, lower hemoglobin, lower serum sodium, and lower albumin. Conclusion The gender difference of long term prognosis of patients with diastolic heart failure is not significant. But the independent predictive factors of patients with different genders are different, thus males and females should be treated accordingly.