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Violent conflict is very old in human society. The development of military technology brought with itself the worst tragedies loss of human live and material devastation in the second half of 20th century in the Horn of Africa. This region is one of the centers of various political violent conflicts in the world, according to length of these violent conflicts, the number of death of people, mainly civilian, refugees and internal displaced persons (IDP). This study elucidates the root causes of long wars in the Horn of Africa focusing mainly on South Sudan and Somalia. It also illustrates how the Super Powers during the Cold War helped their client states to prolong the suffering of people in the region. When Socialist system disappeared from Eastern Europe, Mengistu Haile Mariam's and Siyad Barre's regime ignominiously collapsed. In Ethiopia Amhara power elite, who ruled the Empire state from 1889 to 1991 lost their state power and Tigrian guerrilla fighters captured it through the power of the gun, Eritrea gained its independence from Ethiopia, South Sudan is emerging from long heinous war to independence. The violent conflict in Somalia transformed after the old regime demise in 1991 and the new leaders unable to build new central government. Somalia is fragmented and became the good example of failed state in the theory of contemporary political sociology. The paper tries to explain these complex violent conflicts in this part of Africa.