This review provides an updated overview of recent developments and applications of CE based on previously published reports in the field of omic research. The increased number of published articles on omics shows that the field is growing and attracting the attention of many life science researchers. Due to developments in the omics sciences, many researchers have been studying systems biology, in which biological events in organisms are systematically interpreted through the combination of complex measurements from various methods resulting in high-throughput data. Given the challenges of such complex forms of analysis, CE is a strong candidate for generating omics data useful for acquiring the qualitative and quantitative knowledge necessary for systems-level investigation. By emphasizing CE for systems biology, this review will discuss and focus on the applicability of CE to systems-based analytical data at the genomic, transcriptomic, proteomic, and metabolomic levels from 2005 to the present.