This study estimated greenhouse gas (GHG) and air pollutant emissions from aircraft in the troposphere (aircraft cruise altitudes, 1 - 12 km) over South Korea over a two-year period (2009 - 2010) using an activity-based (Landing and Take-Off (LTO) cycle) methodology. Both domestic and international LTOs covering 4 major airports and 11 smaller airports in South Korea were considered. The annual mean GHG emissions (CO2, N2O, CH4, and H2O) in the troposphere (1 - 12 km) over South Korea during the study period were approximately 3.5 × 103, 3.4 × 10-2, -6.6 × 10-2, and 1.4 × 103 kiloton (kt) yr-1, respectively. The tropospheric air pollutant emissions (CO, NOx, VOCs, and PM2.5) were approximately 3.0, 20, 1.0, and 0.2 kt yr-1, respectively. The monthly GHG and air pollutant emissions showed no significant variations. The GHG and air pollutant emissions during cruises over the South Korean airspace were significant contributors to (e.g., about 80% for NOx and about 75% for CO2) the total national aviation emissions including the emissions at airports, boundary layer and the free troposphere.