Pediatric Central Nervous System (CNS) neoplasms are the second most prevalent tumors of childhood. Further on, prognosis of this type of neoplasms still remain poor and the comprehension of the etiology and pathogenesis of the disease still remains scarce. Several reports have identified microRNAs as significant molecules in the development of central nervous system tumors and propose that they might compose key molecules underlying oncogenesis. In a previous study we have identified several miRNAs, common to different subtypes of pediatric embryonal CNS malignancies as well as, we have identified miRNAs that manifest significant dynamics with respect to their expression and the neoplasmatic subtype. Overall, 19 tumor cases from children diagnosed with embryonal brain tumors were investigated. As controls, children who suffered a sudden death underwent autopsy and were not present with any brain malignancy were used (13 samples of varying localization). Our experimental approach included microarrays covering 1211 miRNAs, which appeared to manifest tumor-specific dynamics. In conclusion, it appeared that certain miRNAs are neoplasm specific and in particular, their expression manifests linear dynamics. Thus, the investigation of miRNA expression in pediatric embryonal brain tumors might contribute towards the discovery of tumor-specific miRNA signatures, which could potentially afford the identification of gene-specific biomarkers related to diagnosis, prognosis and patient targeted therapy, as well as help us understand oncogenetic dynamics.