The availability of completely sequenced genomes and the wealth of literature on gene regulation have enabled researchers to model the transcriptional regulation system of some organisms in the form of a network. In order to reconstruct such networks in non-model organisms, three principal approaches have been taken. First, one can transfer the interactions between homologous components from a model organism to the organism of interest. Second, microarray experiments can be used to detect patterns in gene expression that stem from regulatory interactions. Finally, knowledge of experimentally characterized transcription factor binding sites can be used to analyze the promoter sequences in a genome in order to identify potential binding sites. In this chapter, we will focus in detail on the first approach and describe methods to reconstruct and analyze the transcriptional regulatory networks of uncharacterized organisms by using a known regulatory network as a template.