This paper presents an algorithm to separate the heart sounds, using LabVIEW. The proposed algorithm reads the audio sample signals in.wav format and converts them into a 2-dimentional array. The values stored in this 2-dimentional array and the values of both the separation coefficients are finally fed into the last phase of the algorithm which leads to the separation of heart sounds. After separation, the S1 and S2 signal can be processed in parallel or independently to infer more accurate results. This user friendly technique of separating heart sounds makes it easy for the medical professionals to interpret heart disorders and to further make a better diagnosis. © 2005 - 2012 JATIT & LLS. All rights reserved.