Novel H1N1 flu has spread throughout more than 90 countries on six continents within a short period of less than two months. The World Health Organization thus has declared that this new flu virus has caused a pandemic. The fast spreading of viruses without motherland or borders under accelerated globalization has subverted the concept and construction of the nation-state, which has been practiced in society for a long time. This spreading of the virus blurs the divide between national/international, territory/non-territory, and within borders/without borders. In order to effectively control emerging infectious diseases, the nation-state is forced to engage in trans-regional governance. The issue of trans-regional governance in public health is multi-dimensional and complex. It needs the attention, research and engagement of Taiwan academics. In this article, we conduct a preliminary analysis based on four major questions: Who governs? for whose interests? by what means? and what is the goal?