A 64-year-old man complained of persistent dyspnea and bilateral basi-thoracic pain with shoulder irradiation. Chest computed tomography revealed a heterogeneous left diaphragmatic mass, while magnetic resonance imaging showed hypo-T1 and hyper-T2 signal. Positron-emission tomography did not show any hypermetabolism. Video-assisted thoracic surgery was decided. At inspection, tumour appeared within the posterior costal part of the diaphragmatic muscle. Tumour resection was extended to a 8-cm-long portion of the lumbar part of diaphragm. Diaphragm was repaired with non-absorbable interrupted sutures. Postoperative course was uneventful. Final pathology revealed an intra-diaphragmatic bronchogenic cyst, which is an exceptional condition. Primary diaphragmatic tumours are very rare and preoperative diagnosis cannot be affirmed. Embryologic hypotheses (migration along the oesophagus or envelopment within diaphragmatic precursors of an abnormal supernumerary lung bud) including recent molecular findings of deregulated pathways (fibroblast growth factor-10 and NOTCH) are discussed.