Microvolt T-wave alternans (MTWA), which reflects electrical dispersion of repolarization, is known to be associated with arrhythmia or sudden cardiac death in high risk patients. In this study we investigated the relationship between MTWA and postoperative mortality in 330 cardiac surgery patients. Electrocardiogram, official national data and electric chart were analysed to provide in-hospital and mid-term outcome. MTWA at the end of surgery was significantly associated with in-hospital mortality in both univariate analysis (OR = 27.378, 95% CI 5.616–133.466, p < 0.001) and multivariate analysis (OR = 59.225, 95% CI 6.061–578.748, p < 0.001). Cox proportional hazards model revealed MTWA at the end of surgery was independently associated with mid-term mortality (HR = 4.337, 95% CI 1.594–11.795). The area under the curve of the model evaluating MTWA at the end of surgery was 0.764 (95% CI, 0.715–0.809) and it increased to 0.929 (95% CI, 0.896–0.954) when combined with the EuroSCORE II. MTWA positive at the end of surgery had a 60-fold increase in in-hospital mortality and a 4-fold increase in mid-term mortality. Moreover, MTWA at the end of surgery could predict in-hospital mortality and this predictability is more robust when combined with the EuroSCORE II.