The aim of this study was to identify the risk factors associated with bone grafts infection after cranioplasty. Eighty-four cranioplasties were performed on 75 patients between 2002 and 2006. Cryopreserved bone grafts were used as graft material in group 1 and polymethylmethacrylate (PMMA) was used in group 2. Risk factors including age, gender, time intervals between craniectomy and cranioplasty, mechanism of injury, number of procedures, graft material, and the Glasgow Coma Scale score were compared between groups. Swab culture results and bone graft infection were assessed in group 1. Multiple procedures before cranioplasty and an inadequate time interval between craniectomy and cranioplasty increase the risk of infection after cranioplasty. Swab culture results, age, gender, mechanism of injury, graft material and Glasgow Coma Scale score are not related to infection. The use of PMMA was associated with a relatively low risk of infection (6.25%). Risk of graft infection was not associated with the choice of graft material in the present study. Multiple procedures and insufficient time intervals increase the risk of infection. Interrupting the wound healing process may be the cause of infection. PMMA is a safe material for cranioplasty regardless of previous infection.