A peri-prosthetic joint infection is a feared complication after mega-prosthesis reconstruction of large bone defects. The current study investigates how patients operated with a mega-prosthesis due to sarcoma, metastasis, or trauma, are affected by a deep infection focusing on re-operations, risk for persistent infection, arthrodesis, or subsequent amputation. Time to infection, causative bacterial strains, mode of treatment and length of hospital stay are also reported. A total of 114 patients with 116 prostheses were evaluated, a median of 7.6 years (range 3.8–13.7) after surgery, of which 35 (30%) were re-operated due to a peri-prosthetic infection. Of the infected patients, the prosthesis was still in place in 51%, 37% were amputated, and 9% had an arthrodesis. The infection was persistent in 26% of the infected patients at follow-up. The mean total length of hospital stay was 68 (median 60) days and the mean number of reoperations was 8.9 (median 6.0). The mean length of antibiotic treatment was 340 days (median 183). Coagulase-negative staphylococci andStaphylococcus aureuswere the most frequent bacterial agents isolated in deep cultures. No MRSA- or ESBL-producingEnterobacteraleswere found but vancomycin-resistantEnterococcus faeciumwas isolated in one patient. In summary, there is a high risk for peri-prosthetic infection in mega-prostheses, resulting in persistent infection or amputation relatively often.