Meningiomas arise from the coverings of the brain or the spinal cord. They are mostly benign and can be surgically cured. However, in approximately 5% of the cases, they turn into malignant forms with aggressive clinical behavior and increased risk of tumor recurrence. Cytogenetically meningiomas are well characterized, with normal karyotype or monosomy of chromosome 22 in most tumors and clinically relevant secondary losses of other autosomes and sex chromosomes in a subset of anaplastic tumors. Statistical analyses were performed for 1064 karyotypes derived from 661 meningiomas with respect to progression, and recurrence of the tumor. The order of accumulating genetic aberrations has previously been biostatistically estimated with oncogenetic tree models, and a genetic progression score derived from these models was shown to be predictive for tumor recurrence. Although more homogeneous than other cancer types, meningiomas show considerable intratumoral cytogenetic heterogeneity, particularly in their anaplastic form. We observed different cytogenetic patterns in tumor cells of 224 out of 661 (33.4%) meningiomas. The present study demonstrates that it is not sufficient to consider only the most frequent cytogenetic pattern observed in a sufficient set of cells derived from the same tumor. Even a single cell with more advanced genetic progression may start a clone and indicates also clinical progression. Cox regression analysis reveals that the clone with most advanced progression is a leading marker for recurrence in meningiomas. The aim of this study was the analysis of genetic heterogeneity on single cell basis. Further we investigated if there is a substantial correlation between the intratumoral heterogeneity of a given meningioma and its recurrence risk. We were able to show that the selection of single genetically advanced cells improves the prediction of clinical meningioma progression in a more precise manner.