Metabolic engineering is the directed improvement of cellular properties through the modification of specific biochemical reactions or the introduction of new ones, with the use of recombinant DNA technology. As such, metabolic engineering emphasizes metabolic pathway integration and relies on metabolic fluxes as determinants of cell physiology and measures of metabolic control. The combination of analytical methods to quantify fluxes and their control with molecular biological techniques to implement genetic modifications is the essence of metabolic engineering. Strategies for metabolic flux determination are reviewed in this paper and it is shown how metabolic fluxes can be used in the systematic elucidation of metabolic control in the framework of reaction grouping and top-down metabolic control analysis.