In Indonesia the very foundation of its post-Suharto national policy of `Indonesian Unification` is being shaken to its very core: the Aceh and Papua regions have been involved in separate independence movements; and religious and ethnic tensions have been occurring in Moluccas, Kalimantan, and Celebes regions. Why is large-scale bloodshed continuing to occur after the fall of the Suharto regime? All of this appears to be spontaneous uprisings fueled by the strong resentment and dissatisfaction of the minorities op? pressed during the 32 years of iron-fisted rule of Suharto accompanied by the post-Suharto power vacuum, economic recession and a drive towards democratization. The regional conflicts naturally arose during the process of unifying many island-regions in the archipelago inhabited by a diverse eth- nic population into one country. Moreover, it became an intrinsic element of the Suharto regime`s national policy implementation. Although inhabited by 60% of the nation`s population, Java Island occupies a mere 6.7% of the entire national land area. Therefore, concentrated economic development for Java Island and the subservience of regional governments and public institutions outside Java to the Javanese population have sown the seeds of discontent into the region`s political elite. More? over, the expanded immigration policy implemented for the sake of balanced development of the entire archipelago and regional military defense strategy has caused economic and religious conflicts between the natives and im? migrants of different cultural backgrounds. Although the natives were strongly displeased with the immigration policy, they had to keep silent about the regime`s implementation of the ‘Panca Sila` immigration policy during Suharto`s military rule. This research intends to focus on the explanation of (i) the background information leading up to, (ii) the unfolding of and (iii) each region`s specific cause of the fore-mentioned lengthy regional conflicts following the collapse of Suharto`s power that exacted much human and economic cost. In reality, Indonesia`s regional conflicts cannot be easily explained because each regional conflict has its own compound set of causes. In spite of this, in an attempt to analyze the causes of the conflicts, this research aims to cate- gorize the causes applicable to each region, i.e., inequality in economic development, religious feuds and ethnic feuds.