Ependymomas are common pediatric and adult CNS malignancies with a wide biologic spectrum that is often hard to predict using classic prognostic variables. The molecular pathogenesis is also poorly understood and few reproducible genetic alterations have been identified. The most common genetic alteration has been the loss of the Protein 4.1 family member, NF2, predominantly in spinal ependymomas. In contrast, a pilot study suggested that 4.1B deletions might be more common in intracranial ependymomas. These findings prompted us to study Protein 4.1 family members (NF2, 4.1B, 4.1R, 4.1G) in a larger cohort of 84 ependymomas (51 intracranial and 33 spinal; 11 WHO grade I, 43 grade II, 30 grade III). Fluorescence in situ hybridization was performed using NF2, 4.1B, 4.1R and 4.1G probes and immunohistochemical staining was performed in a subset using merlin, Protein 4.1B and Protein 4.1R antibodies. Additionally, frozen tissue from nine ependymomas (four intracranial and five spinal) was obtained for Western blot analysis for merlin, 4.1B and 4.1R expression. The majority of cases harbored one or more detectable genetic alterations, but we found that 4.1B gene deletions and 4.1R loss of expression were statistically more common in the pediatric vs adult, intracranial vs spinal, and grade III vs grade I/II subsets (P-values of 0.038 to <0.001). Also, 4.1G deletions were seen in 11/27 (41%) patients who either died of disease or had residual/recurrent tumor vs 5/41 patients with no evidence of disease at last follow-up (P=0.009). We conclude that alterations of Protein 4.1 family members are common in ependymal tumors and that specific alterations are associated with distinct clinicopathologic subsets.