BACKGROUND Bronchogenic cysts are lesions of congenital origin derived from the primitive foregut and are the most common primary cysts of the mediastinum. They are most frequently unilocular and contain clear fluid. Respiratory distress is the most common presentation in pediatric patients, manifested by recurring episodes of cough, stridor, wheezing and retractions. METHODS We report the first pediatric case of bronchogenic cyst complicated by atypical Mycobacterium infection. This case describes a 13-year-old Caucasian American female with a large cystic lesion and extensive pulmonary involvement. Pathology studies revealed necrotizing granulomatous inflammation, multiple nodules, and acid-fast bacilli. She was successfully treated with surgical excision and a six-week course of clarithromycin, rifampin and ethambutol. Other unusual aspects of this case include multilocular intraparenchymal cyst appearance, its turbid drainage, and late symptom onset. CONCLUSIONS Bronchogenic cyst should be included in the differential diagnosis of a child with cough, dyspnea, and fever. Although rare, we stress the importance of keeping mycobacterial infection in mind in cases of an infected cyst. Acid-fast culture should be done on sputum and cyst contents. Due to the frequency of negative cultures, stains should also be performed on resected cyst specimens. Antibiotic therapy should be considered and administered based on the extent of infection. All symptomatic or enlarging cysts warrant surgical excision. Prophylactic removal of asymptomatic cysts is recommended due to higher rates of perioperative complications once cysts become symptomatic.