microRNAs (miRNAs) are small non-coding RNAs that cause mRNA degradation and translation inhibition. They are pivotal regulators of development and cellular homeostasis through their control of diverse processes. Recently, great efforts have been made to elucidate many targets that are affected by miRNAs, but the functions of most miRNAs and their precise regulatory mechanisms remain elusive. With more and more matched expression profiles of miRNAs and mRNAs having been made available, it is of great interest to utilize both expression profiles and sequence information to discover the functional regulatory networks of miRNAs and their target mRNAs for potential biological processes that they may participate in. In this chapter, we first briefly review the computational methods for discovering miRNA targets and miRNA-mRNA regulatory modules, and then focus on a method of identifying functional miRNA-mRNA regulatory modules by integrating multiple data sets from different sources. ; Bing Liu, Lin Liu, Anna Tsykin, Gregory J. Goodall, Murray J. Cairns, and Jiuyong Lics