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Deep infection following thoracic aortic replacement is a serious and life threatening complication and successful treatment remains a challenge to surgeons. The infected prosthetic graft should be removed; however, this is not always possible. We report our case, whereby our patient was treated with debridement and omental flap, without removal of the original graft. A 40-year-old male patient underwent ascending aorta replacement due to Stanford type A aortic dissection. The patient complained of fever and chilling 15 days postoperatively and the chest computed tomography (CT) showed fluid collection around the ascending aorta graft. White blood cell count was 13,200 (neutrophil 81%), and blood culture showed no growth. The patient was diagnosed as having a prosthetic graft infection. The sternum was opened, and surrounding tissue was widely debrided. Irrigation with 1% povidone-iodine solution and soaking with 5% povidone-iodine solution was completed as opened sternum status for three days. The omental flap wrapped the graft and filled the sub sternal space, and the sternum was sealed after three days of irrigation. Rifodex was administered for 6 months, and Ciprobay for 9 months. Follow-up chest CT at 1 year postoperatively demonstrated no abnormal findings. Erythrocyte sedimentation rate and C-reactive protein at 22 months postoperatively showed normal ranges. Deep sub sternal infection following a thoracic aorta graft could be treated with an omental flap and conservative care without graft removal.