Cancer or carcinoma is uncontrolled growth of abnormal cells. The transition of normal cell to cancerous cell is very complicated process and the cause of transition varies with situation. Metastasis is the main cause of death in cancer. There are genes which not only promote metastasis but also maintain microenvironment of tumor cells, and initiate the process of epithelium' mesenchymal transition (EMT). MicroRNA (micro RNA) is small, highly conserved noncoding RNAs that control gene expression post-transcriptionally. MicroRNA controls various cellular events like division, differentiation and apoptosis. Their deregulation may result in to cancerous growth. Most (50%) of the microRNA genes are located in the fragile chromosomal regions, which are more susceptible to amplification, deletion or translocation during tumor development. It is predicted that 30% of the all mRNA are directly or indirectly controlled by the microRNA. MetastamiR are that microRNA which have role in regulation of metastasis. MicroRNA expression profile in different cancers showed that it can act as Oncogene as well as Tumor suppressor gene. Till date there are 1921 mature human microRNA sequences registered in miRBase. MicroRNA target prediction is the first step in functional analysis of microRNA. Target prediction is complicated due to partial complementarity between microRNA and its target. There are many target prediction programs available, but the efficiency and sensitivity of these programs are not known. To enhance its efficiency, we need to know problems during prediction. Comparative analysis of different microRNA prediction tools provides an insight into the above parameter. In this study comparative analysis of seven prediction tools is carried out with help of validated microRNA targets of metastatic breast cancer.