While for a long time, negotiating with terrorists was limited to very limited numbers of contexts. After the Good Friday agreement, literature on negotiation with terrorist groups rises. According to this literature, negotiation could be used as means of counterterrorism. This part of conflict resolution literature argues that negotiating with terrorist groups and organizations would culminate in isolating the hardliners and thus reduce the tension and consequently increases the security. This paper would examine the applicability of this argument in Middle East. The paper studies the organizational structure of terrorist groups and then takes Irish Republican Army(IRA) and Al- Qaeda(AQ) as its case studies. With a comparative organizational structure study of IRA as a hierarchical organization and AQ as a network organization, it suggests that using negotiation as counterterrorism measure would be useful when state is facing a terrorist organization with hierarchical structure.