Intellectual disability (ID) is not uncommon in children, but data at the national level are limited, especially those on geographic differences. On the basis of the Disabled Welfare Law, Taiwan began to certify disabled residents and provide various services in 1980. All the cases are registered, and the registry provides a rare opportunity for studying ID at the national level. Using the data from 2004 to 2010, we calculated the prevalence of ID in children by age, gender, and geographic area and assessed the changes over time. We limited analyses to children at least 3 years of age, because certification before 3 years old is discouraged by the government. We found that from 2004 to 2010, the registered cases between 3 and 17 years old ranged from 20,531 to 23,547, and the prevalence of ID increased constantly from 4.40/1000 to 5.79/1000 (p less than 0.01), which generally increased every year in all age groups (p less than 0.01). In each year there were more boy cases than girl cases, and the boy-to-girl ratio generally decreased with age (p less than 0.01 for chi-square test for trend in all years). The prevalence rate ratio ranged from 1.33 to 1.37 (p less than 0.01 in all years), and the changes in the rate ratio were small over the years. We observed a higher prevalence in the rural areas over the years, and the prevalence rate ratio ranged from 1.34 to 1.43 (p less than 0.01 in all years), with an increasing trend over time (p less than 0.01). (Contains 4 tables.)