Factor IXA now a day is becoming attractive target for many researchers for the designing novel anticoagulants. The advances in the computational chemistry can be use full for designing of new chemical entities. The pharmacophore identification and QSAR studies on reported 51 factor IXa inhibitors have been carried out. QSAR model developed considering training and test set approaches with stepwize variable selection method. QSAR models which were further validated for statistical significance and predictive ability by internal and external validation. The hydrogen bond accepter, hydrogen bond donor, positively charged and aromatic carbon are the important features which are contributing towards the activity. The selected best QSAR model A has a training set of 40 molecules and test set of 10 molecules with correction coefficient of 0.9622.