To investigate the greenhouse gases emissions from paddy fields and uplands, methane and nitrous oxide emissions were estimated from local measurement and the IPCC guidelines during 1990-2000 in Taiwan. Annual methane emission from 182,807 to 242,298 ha of paddy field in the first crop season ranged from 8,062 to 12,066 ton, and it was between 16,261 and 25,007 ton for 144,178-211,968 ha in the second crop season with local measurement. The value ranged from 12,132 to 17,465 ton, and from 16,046 to 24,762 ton of methane in the first and second crop season with the IPCC guidelines for multiple aeration treatments, respectively. Annual nitrous oxide emission was between 472 and 670 ton and between 236 and 359 ton in the first and second crop season, respectively. Methane and nitrous oxide emissions from uplands depend on crop, growth season, fertilizer application and environmental conditions. Annual methane emission from upland crops, vegetable, fruit, ornamental plants, forage crops and green manure crops was 138-252, 412-460, 97-100, 3-5, 4-5 and 3-51 ton, respectively. Annual nitrous oxide emission was 1,080-1,976, 1,784-1,994, 2,540-2,622, 31-54, 43-53 and 38-582 ton, respectively. Annual nitrous oxide emission ranged from 91 to 132 ton for 77,593-11,2095 ton of nitrogen-fixing crops, from 991 to 1,859 ton for 3,259,731-6,183,441 ton of non-nitrogen-fixing crops, and from 1.77 to 2.22 Gg for 921,169-1,172,594 ton of chemical fertilizer application. In addition, rice hull burning emitted 19.3-24.2 ton of methane and 17.2-21.5 ton of nitrous oxide, and corn stalk burning emitted 2.1-4.2 ton of methane and 1.9-3.8 ton of nitrous oxide. Methane emission from the agriculture sector was 26421-37914 ton, and nitrous oxide emission was 9810-11,649 ton during 1990-2000 in Taiwan. Intermittent irrigation in paddy fields reduces significantly methane emission; appropriate application of nitrogen fertilization and irrigation in uplands and paddy fields also decreases nitrous oxide emission.