This study is part of a 5-year research project on the national burden of diseases, injuries, and risk factors in Korea. Using disability-adjusted life years (DALYs), a metric introduced by the 1990 Global Burden of Disease (GBD) project, we performed a comprehensive and detailed assessment of the magnitude and distribution of both fatal and non-fatal health problems in the Korean population. The concept and general approach were consistent with the original GBD study, with some methodological modifications to make the study more suitable for Korea. We computed DALYs for 313 causes in both sexes and nine age groups using the entire population's medical records and newly generated Korean disability weights. In 2012, the dominant disease burden was non-communicable diseases, which accounted for 85.21% of total DALYs, while injuries accounted for 7.77% and communicable, maternal, neonatal, and nutritional disorders for 7.02%. Of the total DALYs, 88.67% were from years lived with disability and 11.32% were from years of life lost due to premature mortality. Diabetes mellitus was the leading cause of DALYs, followed by low back pain, chronic obstructive pulmonary disease, ischemic heart disease, ischemic stroke, cirrhosis of the liver, falls, osteoarthritis, motorized vehicle with three or more wheels, and self-harm. The results reported here identify key health challenges and opportunities for future health interventions and policy changes, and provide information that will help assess the major public health issues in Korea, a nation faced with one of the world's most rapidly ageing populations.