The way how to compress ECG data varies from u simple method to a complex method. Because Digital Holter system is not only compressing/saving ECG data but also filtering and diagnosing ECG data. Therefore, the simple algorithm would be better. In this study the algorithm which enables real time compression using templates and AZTEC was investigated. The waveform between R-R peak of the ECG waveform was determined as heat and waveform of which PRD(Percent RMS Difference) are over 50% were determined as new templates. The adequate compression rate and PRD are obtained from the difference between those templates and heats using AZTEC. The algorithm from this study was verified by MIT/B1H database. The experimental results from testing ECG data compression using ten data of CDB showed that the average compression rate was 6.7:1 and the average PRD was 24.5% for the AZTEC algorithm. In case of algorithm from this study, the average compression rate and PRD were 3.3:1 and 13.6%. respectively. Particularly, the errors from the region of QRS complex were smaller than those used by AZTEC, hence the algorithm from this study is considered as a more efficient method diagnosing ECU with QRS Complex.