To investigate the greenhouse gases emissions from paddy fields, methane and nitrous oxide emissions were estimated with the local measurement and the IPCC method during 1990-2006 in Taiwan. Annual methane emission ranged from 9001 to 14,980 ton in the first crop season for 135,314-242,298 ha of paddy fields, and it was between 16,412 and 35,208 ton for 101,710-211,968 ha in the second crop season with the local measurement for intermittent irrigation. The value ranged from 31,122 to 55,729 ton of methane emission in the first crop season, and it was between 29,493 and 61,471 ton in the second crop season with the IPCC guideline for continuous flooding. Annual nitrous oxide emission from paddy fields was between 371 and 728 ton in the first crop season, and the value ranged from 163 to 365 ton in the second crop season with the local measurement. Methane emission from paddy fields in Taiwan for intermittent irrigation was only 26.72-28.92%, 55.65-57.32% and 41.19-43.10% with the IPCC guidelines for continuous flooding and mean temperature of transplanting stage in the first crop, the second crop and total paddy fields, respectively. The values were 53.44-57.84%, 111.29-114.55% and 82.38-86.20% with the IPCC guidelines for single aeration and mean temperature of transplanting stage, respectively; and the values were 133.60-144.61%, 282.56-286.62% and 205.96-215.49% with the IPCC guidelines for multiple aeration and mean temperature of transplanting stage, respectively. Intermittent irrigation in paddy fields reduces methane emission significantly; appropriate application of nitrogen fertilizer and irrigation in paddy fields also decreases nitrous oxide emission. (C) 2008 Published by Elsevier Ltd.