Metabolomics represents a global quantitative assessment of metabolites within a biological system. The metabolic analysis of cell cultures has many potential applications and advantages to currently used methods for cell line testing. Metabolite concentrations represent sensitive markers of both genomic and phenotypic changes. Consequently, the development of robust metabolomic platforms will greatly facilitate various applications of cell cultures - including, for example, the understanding of the in vitro and in vivo actions of drugs - and aid in their rapid incorporation into novel therapeutic settings. In addition, metabolomic analysis of cell lines provides information, either independently or in conjunction with other omics measurements, essential for system level analysis and modeling of biological systems. This review outlines some of the applications of metabolomics in cell culture analysis and some of the issues that need to be addressed to make this approach more relevant.