Bioinformatics-based applications have been incorporated into several medical disciplines, including cancer, neuroscience, and recently psychiatry. Both the increasing interest in the molecular aspect of neuropsychiatry and the availability of high-throughput discovery and analysis tools have encouraged the incorporation of bioinformatics and neurosystems biology techniques into psychiatry and neuroscience research. As applied to neuropsychiatry, systems biology involves the acquisition and processing of high-throughput datasets to infer new information. A major component in bioinformatics output is pathway analysis that provides an insight into and prediction of possible underlying pathogenic processes which may help understand disease pathogenesis. In addition, this analysis serves as a tool to identify potential biomarkers implicated in these disorders. In this chapter, we summarize the different tools and algorithms used in pathway analysis along with their applications to the different layers of molecular investigations, from genomics to proteomics.