Objective The objective of this study was the economic evaluation of screening school children for congenital heart disease (CHD). Methods The sample consisted of all the 45 725 students in grades 1 and 7 from Taichung County, Taiwan. STATISTICA, version 7.1, was used to determine descriptive statistics and Student's t tests on students' height, weight, and body mass index (BMI). Results The total cost of CHD screening was NT$4 863 866 (NT$32 = US$1), and the average cost was NT$106.37 per child. The rate of finding new asymptomatic students was 2.9174%, and the cost of finding 1 asymptomatic student was NT$3646. Also, a cost-effective analysis showed NT$165.7 per year of life saved. Conclusions Twelve Student's t tests were conducted, and it found that students' height, weight, and BMI was not associated with asymptomatic students. A goodness-of-fit χ2 found that females have a higher rate of asymptomatic CHD.