We stand at the dawn of the next great period of natural products research. We now have tools to begin unraveling the chemical and physiological mechanisms by which these phytochemicals affect the function of living cells, both in plants and animals. The advances in analytical research will allow us to better use these compounds in the control of diseases in both plants and animals. This chapter used the analysis of soy isoflavones to illustrate the approaches to natural product research, but these principles can be applied to nearly any of the phenolic compounds found in plants.