MicroRNAs (miRNAs) are small (16-24 nucleotides) noncoding RNAs that negatively regulate gene expression. Growing evidence demonstrates that miRNAs participate in the regulation of numerous physiological and pathological processes. The clinical utility of the cell-type-specific miRNA expression profile (miRomics) has been directly demonstrated in molecular classification of tumor samples and in prediction of prognosis or therapeutic responsiveness. Identification of the relevant miRNAs and their targets requires both in silico and molecular biological methods. In this review, we summarize the methodological arsenal used in miRNA-related research, and through our own data on adrenal tumors, we present how miRNA could be integrated into omics-based networks. The expanding knowledge obtained from miRNA research may lead to the development of novel diagnostic and treatment modalities in future.