Abstract Objective The best material choice for cranioplasty following craniectomy remains subject to discussion. Complication rates after cranioplasty tend to be high. Computer-assisted 3-dimensional modeling of polyetheretherketone (PEEK) was recently introduced for cranial reconstruction. The aim of this study was to evaluate patient- and surgery-related characteristics and risk factors that predispose patients to cranioplasty complications. Material and methods This retrospective study included a total of 40 cranial PEEK implants in 38 patients, performed at two reference centers in the Netherlands from 2011 to 2014. Complications were registered and patient- and surgery-related data were carefully analysed. Results The overall complication rate of PEEK cranioplasty was 28%. Complications included infection (13 %), postoperative hematoma (10 %), cerebrospinal fluid leak (2.5 %) and wound-related problems (2.5 %). All postoperative infections required removal of the implant. Nonetheless removed implants could be successfully re-used after re-sterilization. Conclusion Although overall complication rates after PEEK cranioplasty remain high, outcomes are satisfactory, as our results compare favourably to recent literature reports on cranial vault reconstruction.