Approximately 9 million cases of tuberculosis (TB) are reported annually and half a million occur in children <15 years of age. Globally, TB notifications in children have been neglected for decades although childhood TB may represent a sentinel for ongoing transmission. Data included in this study were collected from the TB database of the Swiss Federal Office of Public Health, which includes culture-confirmed TB and/or cases treated with ≥3 anti-mycobacterial drugs. Data from all children <15 years of age reported between 1996 and 2011 were analyzed. A total of 320 cases of TB (166 cultures confirmed, 5 confirmed by nucleic acid amplification, 149 other than definite cases) were reported with an overall incidence rate of 1.6 per 100,000 children (range 1.2-2.2). A total of 154 (48 %) children were younger than 5 years of age and 141 (44 %) were born in Switzerland. Children below 5 years of age were more likely to be Swiss-born compared to children aged 10 to 14 years (74 % versus 26 %). When analyzing the country of origin, only 55 children (17 %) were of Swiss origin. Of all children with foreign origin, 117 (47 %) were from a country within the WHO European Region. In 288 (90 %) of all notified cases, the site of disease was the lung. Mycobacterial culture was positive in 166 cases (51.9 %) with 1.8 % multi-drug-resistance. The overall incidence of childhood TB disease reported in Switzerland remained stable over a 16-year period with a remarkable high rate of very young patients of foreign origin. Only half of the reported cases were culture confirmed, highlighting the need for better diagnostic tests in childhood TB.