In spite of numerous studies concerning the pathogenesis of pilocytic astrocytoma (PA), the exact mechanism of the process still remains undetermined. It is difficult to obtain concordance between particular studies, which makes review of existing data especially troublesome. Nevertheless, the most important causative factors seem to be NF1 gene inactivation, in cases related to neurofibromatosis type 1, and BRAF gene overexpression in sporadic PAs, both resulting in MAPK/Erk pathway upregulation. Other molecular alterations, like mTOR or PI3K pathway deregulation, or Matrilin 2 overexpression, may influence the course of the disease, leading to the development of more aggressive and recurrent tumors. In the current paper we review genetic alterations in PA and describe currently studied molecular markers that may contribute to the development of the tumor and can be used in pathological staging of the malformation.