Pharmaceutic studies require to analyze thousands of ECGs in order to evaluate the side effects of a new drug. In this paper we present a new support system based on the use of probabilistic models for automatic ECG segmentation. We used a bayesian HMM clustering algorithm to partition the training base, and we improved the method by using a multi-channel segmentation. We present a statistical analysis of the results where we compare different automatic methods to the segmentation of the cardiologist as a gold standard.