Background: Appropriate diagnosis and treatment of latent tuberculosis infection (LTBI) play the most important role in the control of tuberculosis. This study aimed to determine the prevalence of LTBI among healthy tuberculosis unexposed children vaccinated with BCG using the tuberculin skin test (TST) and QuantiFERON TB Gold In-Tube (QFT-GIT) and comparing the agreement between the two tests. Methods: A cross-sectional study was carried out between October 2009 and March 2010 in 24 schools and 11 daycare centers. A total of 967 children were divided into 15 age groups, with a minimum of 64 children per group.Results: The prevalence rates of LTBI with TST were 3.8%, and 2.2% with QFT-GIT. One case was positive in TST and QFT-GIT, 20 cases were QFT-GIT positive, but TST negative and 36 cases were TST positive, but QFT-GIT negative, and finally, 910 cases were negative in both. There was poor agreement between TST and QFT-GIT (1.8%, 95%, CI: 0%-5.3%, k=0.007). The specificity of QFT-GIT in the BCG vaccinated, children aged 1-15 years old, was 97.8% (97.8%, 95% CI: 96.8%-98.8%). After three months, 2/17 (11.8%) of those initially QFT-GIT negative converted, and 10/15 (66%) of those initially QFT-GIT positive reverted.Conclusion: It seems that TST and QFT-GIT are not appropriate tests for the diagnosis of LTBI among healthy tuberculosis unexposed BCG vaccinated children. There was a low reproducibility rate of QFT-GIT. The cause of the the poor agreement requires further studies.