Objective To assess the value of fiberobronchoscopy in the diagnosis of endobronchial tuberculosis. Methods A total of 67 children suspected of endobronchial tuberculosis in our ward from March 2010 to December 2012 had been tested by chest CT and fiberobronchoscopy, mycobacteria culture, liquid-based interlayer vessel technique and FQ-PCR from bronchoalveolar lavage fluid and biopsy. Results 50 patients were clinically diagnosed as endobronchial tuberculosis. The positive rate of FQ-PCR (60%) and liquid-based interlayer vessel technique (42%) are higher than that of mycobacteria culture (20%), which showed no significant difference with biopsy. The positive rate of the combined detection (FQ-PCR and liquid-based interlayer vessel technique) is significantly higher than that of mycobacteria culture and biopsy. Conclusions Fiberobronchoscopy is effective for the diagnosis of endobronchial tuberculosis.