Endobronchial ultrasound guided transbronchial needle aspiration (EBUS-TBNA) has recently been shown to be accurate in diagnosis and staging of mediastinal lymph node metastases. We report a case of squamous cell carcinoma diagnosed by endobronchial biopsy with concomitant contralateral hilar lymph node metastasis from small cell carcinoma being confirmed by EBUS-TBNA. The diagnosis of synchronous primary lung cancers in this case, which altered the treatment strategy, would not be made if pathological staging of intrathoracic lymph node was not pursued. The unique role of EBUS-TBNA in diagnosis of hilar lymphadenopathy was underscored. The potential pitfall of missing synchronous lung tumour if the diagnosis is based either on sampling from intrathoracic lymph node or from endobronchial lesion alone is discussed.