Since 1995 the Korean Ministry of Science and Technology has introduced and implemented a project based system (PBS) for awarding R&D funds. While capital investments for national laboratories such as buildings and research facilities are supported by the government, normal operating expenses including personnel expenses should be earned by national laboratories through open competition under PBS. The project budget includes both direct research costs and indirect costs. The purpose of this paper is to examine the components of indirect costs and to examine determinants of indirect costs of national laboratories in Korea. The indirect costs of nineteen national laboratories are examined. The direct personnel costs and indirect personnel costs out of total personnel costs are 72% and 28%, respectively. The average indirect cost rate is 74.1% of direct personnel costs. Major components of indirect costs are general operating costs, indirect personnel costs, taxes and dues, and expenses related to the usage of equipment. The significant determinants of indirect cost are indirect personnel ratio. the ratio of unique projects, the type of national laboratories (pure research laboratories or other), and asset activity ratio measured as research divided by total assets. The high indirect personnel ratio, the high ratio of unique projects, the laboratories classified as other, the low asset activity ratio are related to high indirect cost rates.