Recently, Indonesia has experienced six major provincial, civil, armed conflicts. Underlying causes include the transmigration policy, sectarian disputes, the Asian economic crisis, fall of authoritarian rule, and a backlash against civil and military abuses. The public health impact involves the displacement nationwide of > 1.2 million persons. Violence in the Malukus, Timor, and Kalimantan has sparked the greatest population movements such that five provinces in Indonesia each now harbor > 100,000 internally displaced persons. With a background of government instability, hyperinflation, macroeconomic collapse, and elusive political solutions, these civil armed conflicts are ripe for persistence as complex emergencies. Indonesia has made substantial progress in domestic disaster management with the establishment of central administrative authority, strategic planning, and training programs. Nevertheless, the Indonesian experience reveals recurrent issues in international humanitarian health assistance. Clinical care remains complicated by absences of treatment protocols, inappropriate drug use, high procedural complication rates, and variable referral practices. Epidemiological surveillance remains complicated by unsettled clinical case definitions, non-standardized case management of diseases with epidemic potential, variable outbreak management protocols, and inadequate epidemiological analytic capacity. International donor support has been semi-selective, insufficient, and late. The militia murders of three UN staff in West Timor prompted the withdrawal of UN international staff from West Timor for nearly a year to date. Re-establishing rules of engagement for humanitarian health workers must address security, public health, and clinical threats.