INTRODUCTION: Cranioplasty (CP) after decompressive craniectomy (DC) is a common neurosurgical procedure. Implementation of European Union (EU) directives recommending bacterial cultures before cryopreservation, lead to increased number of autologous bone flaps being discarded due to positive cultures. A new method for handling bone flaps prior to cryopreservation, including the use of pulsed lavage, was developed. RESEARCH QUESTION: The aim was to evaluate the effect of a new method on proportion of positive bacterial cultures and surgical site infection (SSI) following CP surgery. MATERIAL AND METHODS: Sixty-one bone flaps from 53 consecutive DC surgery patients were retrospectively included and the study period was divided into before and after method implementation. Patient demographics, laboratory and culture results, type of CP and occurrence of SSI were analyzed. RESULTS: Twenty-six and 18 bone flaps were available for analysis during the first and second period, respectively. The proportion of positive bacterial cultures was higher in the first period compared to the second (n ​= ​9(35%) vs 0(0%); p ​= ​0.001), and thus the use of custom made implants was considerably higher in the first study period (p ​= ​0.001). There was no difference in the frequency of post-cranioplasty SSI between the first and second study period (n ​= ​3 (11.5%) vs 1 (4.8%), p ​= ​0.408). DISCUSSION AND CONCLUSION: The new method for handling bone flaps resulted in a lower frequency of positive bacterial cultures, without increased frequency of post-cranioplasty SSI, thus demonstrating it is safe to use, allows compliance with the EU-directives, and may reduce unnecessary discarding of bone flaps.