What explains variation in institution-building under foreign occupations? Why do some state-building missions produce effective and durable state institutions, while others leave a legacy of weak or dysfunctional ones? I explored these questions through a comparative study of the Japanese colonization of Taiwan (1895-1945) and the American colonization of the Philippines (1898-1941), which produced contrasting institutional legacies despite the presence of similar initial conditions. While a strong bureaucratic Taiwanese state arose in the aftermath of Japanese colonization, the legacy of the American occupation of the Philippines was a weak postcolonial state penetrated by parochial interests. I explain variation in institution-building outcomes through two causal variables: (i) the degree of discretionary power afforded to the occupational administration by the home government; and (ii) the ability of native elites to effectively resist the institution-building effort. Discretionary power allows reform agents to abandon any pre-formulated (and likely ill-conceived) plans, and instead flexibly integrate native laws, norms, and customs with their new institutional designs. Additionally, and contrary to conventional wisdom, more effective institutions emerge when native elites possess the willingness and capacity to resist (even violently) the institution-building effort of foreign agents. The reformist state-building agenda of occupiers is likely to be in direct opposition to the distributional interests of native elites, who seek to maintain their advantageous position within the existing order. It is, therefore, only under the threat of effective resistance that foreign agents will accommodate the interests of native elites to forge institutions with local ownership. The main empirical chapters of the dissertation draw on more than two years of original archival research in fourteen libraries and depositories across Japan, Taiwan, and the United States. In both cases, my analysis focused on the similarities and differences in the process through which education and police institutions were developed over time; these two areas were chosen due their importance for a country's political stability and socioeconomic development. The applicability of conclusions drawn from the historical cases to contemporary state-building missions was assessed through an examination of recent U.S. efforts at building a police institution in Afghanistan.