Background The cost of treating infection after hip and knee arthroplasty is well documented in the literature. The purpose of this study was to determine the cost of two-stage reimplantation for deep infection after shoulder arthroplasty. Methods Between 2003 and 2012, 57 shoulders (56 patients) underwent a two-stage reimplantation for deep periprosthetic shoulder infection; implants placed at reimplantation included anatomic total shoulder arthroplasty (a-TSA) in 58%, reverse total shoulder arthroplasty (r-TSA) in 40%, and hemiarthroplasty (HA) in 2%. During the same timeframe, 2953 primary shoulder arthroplasties (2589 patients) were performed at the same institution (a-TSA in 55%, r-TSA in 28%, and HA in 17%). Total direct medical costs were calculated by using standardized, inflation-adjusted costs for services and procedures billed during hospitalization and were adjusted to nationally representative unit costs in 2013 inflation-adjusted dollars. Results The mean hospital cost (per shoulder) for two-stage reimplantation was $35,824 (95% CI: 33,363 to 38,285) and was significantly higher than for primary procedures (mean: $16,068; 95% CI: 15,823 to 16,314). Both Part A and Part B costs were significantly higher in two-stage reimplantation (p