Aim To determine the metabolic changes in rats with heart failure by the application of proteomics, in order to discover possible new therapeutic targets. Methods Myocardial infarction model was established by left anterior descending coronary artery ligation. 4 weeks after operation, left ventricular ejection fraction was about 46.4%±10.9%. Then it was used as heart failure model. The rats were killed, left ventricular was cut off and the mitochondrial protein was extracted. Weight-age matched rats acted as control. The mitochondrial protein expression in the two groups was analyzed by two-dimensional gel electrophoresis. Results 3 protein spots altered significantly and they were exercised, washed and analyzed by using liquid chromatography-mass spectrometry. Aldehyde dehydrogenase-2 (ALDH-2) was identified using database comparision. Expression of ALDH-2 decreased remarkably in heart failure group compared with control. Furthermore, ALDH-2 mRNA expression of rats was detected at 3, 7, 14 and 28 d after lactate dehydrogenase ligation, which decreased gradually after operation as a result. Conclusions Mitochondrial ALDH has recently been identified as the enzyme that convert nitroglycerin into nitrate. The decreased expression of ALDH-2 in rats with heart failure may provide a clue for nitroglycerin tolerance in patients with heart failure.