Case detection, diagnosis and treatment of tuberculosis (TB) in children are challenging issues worldwide. This study in Afghanistan aimed to evaluate paediatric TB case management, including contact investigation, at health facilities where all diagnostic processes were available. In 7 out of 8 regions of the country 1 province was selected. Documents used for management of paediatric TB cases were reviewed in 15 distinct hospitals and 8 provincial hospitals in the selected provinces. The key issues which emerged were: a low suspect rate among total outpatients (0.4%) and a very low suspect rate among children aged < 5 years; low performance of suspect management (68.5% suspects received further examinations); low utilization of other diagnostic methods; a high early defaulter rate (14.0%); and insufficient coverage of contact management (74.0%). This survey indicated that the Afghanistan national TB programme needs to develop plans to improve the quality of diagnosis, suspect management and contact management in paediatric TB cases.