The objective was to assess the annual risk of tuberculosis infection by means of tuberculin skin testing (TST) in children, evaluating whether QuantiFERON-TB Gold In-Tube (QFN-G-IT) could improve the accuracy. On the basis of the positive TST results, the global annual incidence was estimated at 0.78%, with an increase in the prevalence from 0.64% to 1.68% in 2 years. However, QFN-G-IT was only positive in 6 of the 25 children with positive TST. The confirmation of the positive TST results by QFN-G-IT provided more accurate annual incidence estimation.