Microarray technology has become a widely used tool for analyzing the expression of tens of thousands of genes simultaneously on high-density microarrays in a single experiment, together with the availability of the complete nucleotide sequence of the human genome. DNA microarray technologies are powerful tools in the laboratory setting for scientific research, hypothesis generation, and the production of leads for subsequent validation through more sophisticated technologies. Since 2002, and particularly in the past few years, the utility of various DNA microarray technologies in endometriosis has rapidly and tremendously evolved; DNA microarray studies provide extremely important information that enable a better understanding of pathophysiology and disease etiology. This is a review of the literature focused on new findings of endometriosis pathophysiology obtained using various microarray technologies: gene expression profiling, microarray-based comparative genomic hybridization (CGH) (array CGH) single nucleotide polymorphism (SNP) arrays, the combination of chromatin immunoprecipitation (ChIP) with hybridization of microarrays (ChIP-on-chip). The present review discusses the results of a decade of DNA microarray technology experience, with emphasis on the pathophysiology of endometriosis in the context of clinical studies.