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Background  Childhood tuberculosis (TB) has been neglected in the fight against TB. Despite implementation of Directly Observed Treatment Shortcourse (DOTS) program in public and private hospitals in Indonesia since 2000, the burden of childhood TB in hospitals was largely unknown. The goals of this study were to document the caseload and types of childhood TB in the 0-4 and 5-14 year age groups diagnosed in DOTS hospitals on Java Island, Indonesia.    Methods  Cross-sectional study of TB cases recorded in inpatient and outpatient registers of 32 hospitals. Cases were analyzed by hospital characteristics, age groups, and types of TB. The number of cases reported in the outpatient unit was compared with that recorded in the TB register.    Results  Of 5,877 TB cases in the inpatient unit and 15,694 in the outpatient unit, 11% (648) and 27% (4,173) respectively were children. Most of the childhood TB cases were under five years old (56% and 53% in the inpatient and outpatient clinics respectively). The proportion of smear positive TB was twice as high in the inpatient compared to the outpatient units (15.6% vs 8.1%). Extra-pulmonary TB accounted for 15% and 6% of TB cases in inpatient and outpatient clinics respectively. Among children recorded in hospitals only 1.6% were reported to the National TB Program.    Conclusion  In response to the high caseload and gross under-reporting of childhood TB cases, the National TB Program should give higher priority for childhood TB case management in designated DOTS hospitals. In addition, an international guidance on childhood TB recording and reporting and improved diagnostics and standardized classification is required

High caseload of childhood tuberculosis in hospitals on Java Island, Indonesia: a cross sectional study