Heart sound segmentation into its components, S1, systole, S2 and diastole is the first step of analysis and the most important part in the automatic diagnosis of heart sounds. Conventionally, the Shannon energy envelope peak detection method has been popularly used due to its superior performance in locating S1 and S2. Recently, the HMM has been shown to be quite suitable in modeling the heart sound signal and its use in segmenting the heart sound signal has been suggested with some success. In this paper, we compared the two methods for heart sound segmentation using a common database. Experimental tests carried out on the 4 different types of heart sound signals showed that the segmentation accuracy relative to the manual segmentation was 97.4% in the HMM based method which was larger than 91.5% in the peak detection method.