The mechanisms by which polyphenols and their metabolites alter the functions of cells (proliferation, differentiation, and apoptosis) is of great interest as investigators explore their roles in the prevention of disease. DNA microarray analysis is a widespread technology that provides a glimpse of global gene expression. It may provide important perspectives in polyphenols research, involving new leads for further scientific investigation. However, what are its limitations? Are the statistics used in the analysis of microarray data fundamentally sound? Do we really know how to approach the analysis of a system? These topics are discussed along with some recent applications of microarray analysis to polyphenols research.