We examine what determines the flow of foreign direct investment (FDI) in Indonesia, focusing on the role of institutional measures. A knowledge-and-physical-capital (KPC) model is applied to a panel dataset that covers 42 of Indonesiaâ€™s FDI partners from 2004 to 2012. Evidence shows that both horizontal and vertical FDIs coexist in the bilateral aggregate data of Indonesiaâ€™s FDI flows, but horizontal FDI appears to be dominant. This can be explained by the market size (proxied by the total GDP of both countries and similarity in incomes per capita) and the relative factor endowments (proxied by skilled labor and physical capital). The vertical FDI, on the other hand, could be only explained by the significant effect of unskilled labor. Institutional factors, particularly corruption, are apparently important in affecting Indonesiaâ€™s bilateral FDI flows. The results also show that a higher FDI level in Indonesia positively correlates with macroeconomic factors, open policy factors, and utility infrastructure factors.