Background: Deep infection of the shoulder following rotator cuff repair is uncommon. There are few reports in the literature regarding the management of such infections. Methods: We retrospectively reviewed the charts of thirteen patients and recorded the demographic data, clinical and laboratory findings, risk factors, bacteriological findings, and results of surgical management. Results: The average age of the patients was 63.7 years. The interval between the rotator cuff repair and the referral because of infection averaged 9.7 months. An average of 2.4 procedures,were performed prior to referral because of infection, and an average of 2.1 procedures were performed at our institution. All patients had pain on presentation, and most had a restricted range of motion. Most patients were afebrile and did not have an elevated white blood-cell count but did have an elevated erythrocyte sedimentation rate. The most common organisms were Staphylococcus epidermidis, Staphylococcus aureus, and Propionibacterium species. At an average of 3.1 years, all patients were free of infection. Using the Simple Shoulder Test, eight patients stated that the shoulder was comfortable,vith the arm at rest by the side, they could sleep comfortably, and they were able to perform activities below shoulder level. However, most patients had poor overhead function. Conclusions Extensive soft-tissue loss or destruction is associated with a worse prognosis. Extensive debridement, often combined with a muscle transfer, and administration of the appropriate antibiotics controlled the infection, although most patients were left with a substantial deficit in overhead function of the shoulder.