Diagnosis of bronchogenic cysts is possible with computed tomography, but half of all cases present as soft tissue densities. Two such cases are highlighted where asymptomatic bronchogenic cysts that presented as soft tissue masses were evaluated by endobronchial ultrasound (EBUS). After studying the ultrasound image characteristics, the diagnosis was confirmed using EBUS-guided transbronchial needle aspiration (EBUS-TBNA). The first case had ultrasound findings of an anechoic collection, and the aspirate was serous with negative microbiologic cultures. The second was an echogenic collection within a hyperechoic wall. Needle aspirate was purulent and cultured Haemophilus influenza. The diagnosis of a bronchogenic cyst complicated by infection was made, and the lesion was surgically resected. This potential for EBUS in the diagnosis of bronchogenic cysts and in identifying complications such as infection should be considered in the management of such cases.