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Surgical site infections (SSIs) occur in approximately 700 pediatric patients annually and are associated with increased morbidity, mortality and cost. The aim of this study is to determine risk factors for SSI among pediatric patients undergoing craniotomy and spinal fusion.This is a retrospective case-control study. Cases were craniotomy or spinal fusion patients with SSI as defined by Centers for Disease Control and Prevention criteria with surgery performed from January 1, 2008 to July 31, 2009. For each case patient, 3 uninfected controls were randomly selected among patients who underwent the same procedure as the case patient within 1 month. We performed analyses of risk factors for craniotomy and spinal fusion SSI separately and as a combined outcome variable.Underweight body mass index, increased time at lowest body temperature, increased interval to antibiotic redosing, the combination of vancomycin and cefazolin for prophylaxis, longer preoperative and postoperative intensive care unit stay and anticoagulant use at 2 weeks postoperatively were associated with an increased risk of SSI in the combined analysis of craniotomy and spinal fusion. Forty-seven percent of cases and 27% of controls received preoperative antibiotic doses that were inappropriately low because of their weight.We identified modifiable risk factors for SSI including antibiotic dosing and body temperature during surgery. Preoperative antibiotic administration is likely to benefit from standard processes. Further studies of risk benefit for prolonged low body temperature during procedures are needed to determine the optimal balance between neuroprotection and potential immunosuppression associated with low body temperature.