BACKGROUND Clinical investigations of childhood tuberculosis (TB) are challenged by the paucibacillary nature of the disease and the difficulties in obtaining specimens. We investigated the challenges in diagnosing TB in children in a low-incidence country. METHODS The data were retrieved retrospectively from the paediatric departments at Danish university hospitals from April 2004 to March 2009 using the diagnosis code A15.0-A19.9 in children below the age of 15 years. RESULTS A total of 54 children were identified of whom 13 were native Danes. The remaining immigrants were from a range of countries, the majority from Somalia. In all, 44 children had pulmonary TB and the proportion of extrapulmonary TB was higher among immigrants than among Danes. The cardinal symptoms were fever, weight loss and cough. In 41 cases (76%), a combination of a positive tuberculin skin test, an abnormal chest X-ray and the clinical presentation led to initiation of treatment. TB diagnosis was confirmed later by culture in 29 cases. The median number of days from contact to the healthcare system to treatment initiation was two days for 23 children who were part of contact tracing and seven days for the remaining children. All children but one completed treatment, and three patients were retreated due to relapse. Side effects to treatment were observed in 20 cases. None of the patients died. CONCLUSIONS The majority of the children affected with TB were foreign-born with a higher proportion of extrapulmonary TB. The microbiological confirmation was low. A rapid onset of treatment was closely related to known, recent exposure.