MicroRNAs (miRNAs) are important regulators of gene expression in virtually all eukaryotic cell types including the diverse cell types found in the CNS. They are involved in repressing gene expression by complementary hybridization to cognate protein-coding mRNAs. The likely involvement of miRNAs in disease processes requires both accurate detection and expression analysis strategies. In comparison to conventional methodologies to study miRNA expression, microar-rays offer an advantage in terms of throughput, sensitivity and specificity. Although microarrays are almost routinely used in laboratories for the analysis of mRNA, the small size of miRNAs presents challenges for their analysis in terms of probe design, target labeling and hybridization conditions. We discuss these issues in this chapter as well as highlighting the emerging perspectives in this field.