Since the development of endobronchial ultrasound-guided real-time needle aspiration (EBUS-rt-TBNA) no false positive (FP) cases have been described. We present the first FP case for EBUS-rt-TBNA secondary to a carcinoma in situ (CIS) in the bronchial point of puncture. A 66-years-old male was referred to our Institution because of a mass in left lower lobe. The bronchoscopy did not show any endobronchial lesion. The cytology of the washing confirmed an unspecified non-small cell lung cancer. An EBUS-rt-TBNA for staging was carried out. No mediastinal nodes over 5 mm length were found but one single left hilar node at station 11 L was sampled. The cytology of the TBNA showed lymphocytes and neoplastic squamous cells. The patient underwent thoracotomy. On the surgical specimen no metastasis on any of the nodes resected were detected but a CIS on the bronchial resection margin was described. A bronchial biopsy confirmed CIS on the bronchial stump. The reported case depicts an unusual situation, we consider EBUS-rt-TBNA an accurate technique if minimal requirements are met.