Childhood tuberculosis (TB) is difficult to diagnose and there are no standardised case definitions. TB records of patients aged >5 years reported in Northern Portugal between 2000 and 2009 were reviewed. Of the 116 children diagnosed with TB, 72 (62.1%) were male; the mean age was 2.2 ± 1.2 years. Of the 32 children (27.6%) with confirmed TB, only 46.7% had provided samples for culture, showing that little effort is made to obtain specimens for confirmation. We could not identify independent factors associated with the low rate of sample collection or anti-tuberculosis treatment without confirmation; chest radiography lesions were less frequent in children who began treatment without confirmation (adjusted OR 0.23, 95%CI 0.05-0.98).