Tracking of repolarization instabilities in the ECG, such as T-wave alternans (TWA), has become a popular non-invasive method to assess the vulnerability to malignant arrhythmic events. These instabilities are usually characterized by small amplitude changes and their measurement is difficult due to the presence of noise and artifacts. Several methods have been recently proposed to address this problem. Most of them are based on amplitude analysis of beat-to-beat alternation of the T wave. This paper describes a preprocessing stage intended to be used prior to amplitude analysis and aimed at improving the alignment between consecutive T waves. This increases the accuracy of the difference calculation.