Metabolomics, the ‘global’ study of metabolite changes in a biological system, has drawn a significant amount of interest over the last few years. It can be said to be an amalgam of traditional areas such as metabolite analysis, bioanalytical development and chemometrics. Thus, piecing these areas together into the cohesive science of metabolome analysis has proved to be difficult. Most work to date has been focused on plant, microbial, as well as tissue and biofluid samples. However, the diverse potential of metabolomics in many fields, including cell engineering, has made it a universal tool for industrial, medical and research purposes. It is also a vital component of a ‘systems biology’ approach, as it is believed to be a good reflection of the phenotype of any cell or tissue. At the heart of metabolomics’ growth is the issue of method development, including sample preparation, instrument analysis, data processing and bioinformatics. Here, we look at the cell-culture applications of metabolomics and the issues that can transform metabolomics into a mature ‘omics’ science.