In patients who have undergone decompressive craniectomy, autologous bone flap reinsertion becomes necessary whenever the cerebral situation has consolidated. However, aseptic necrosis of the bone flap remains a concern. The aim of this study was to report possible perioperative complications in patients undergoing autologous bone flap reinsertion and to identify the risk factors that may predispose the bone flap to necrosis. All patients admitted to the authors' neurosurgical department between September 1994 and June 2011 and who received their own cryoconserved bone flap after decompressive craniectomy were studied. The grade of the bone flap necrosis was classified into 2 types. Type II bone necrosis was characterized by aseptic resorption with circumscribed or complete lysis of tabula interna and externa requiring surgical revision. To define predisposing factors, a multivariate analysis was performed using bone necrosis as the dependent variable. Among the 372 patients (mean age 48.6 years, 57.4% males) who received 414 bone flaps during the observation period, 134 (36.0%) had a diffuse traumatic brain injury, 69 (18.5%) had subarachnoid hemorrhage, 58 (15.6%) had cerebral infarction, 56 (15.1%) had extraaxial bleeding, 43 (11.6%) had intracerebral bleeding, and 12 (3.2%) had a neoplasm. Surgical relevant Type II bone flap necrosis occurred in 85 patients (22.8%) and 91 bone flaps, after a median time of 15 months (interquartile range [IQR], 10-33 months). In a multivariate analysis with Type II necrosis as the dependent variable, bone flap fragmentation with 2 (OR 3.35, 95% CI 1.59-7.01, p < 0.002) or more fragments (OR 24.00, 95% CI 10.13-56.84, p < 0.001), shunt-dependent hydrocephalus (OR 1.76, 95% CI 0.99-3.12, p = 0.04), and a younger age (OR 0.98, 95% CI 0.96-0.99, p = 0.004) was associated with a higher risk for the development of an aseptic bone flap necrosis. In patients undergoing bone flap reinsertion after craniotomy, aseptic bone necrosis is an underestimated problem during long-term follow-up. Especially in younger patients with an expected good neurological recovery and a fragmented bone flap, an initial allograft should be considered because of an increased risk for aseptic bone flap necrosis.