In this research, we apply clustering techniques to the malware detection problem. Our goal is to classify malware as part of a fully automated detection strategy. We compute clusters using the well-known �-means and EM clustering algorithms, with scores obtained from Hidden Markov Models (HMM). The previous work in this area consists of using HMM and �-means clustering technique to achieve the same. The current effort aims to extend it to use EM clustering technique for detection and also compare this technique with the �-means clustering