DNA microarrays, initially designed to measure gene expression levels, also provide an ideal platform for determining genetic diversity. Oligonucleotide microarrays, predominantly high-density oligonucleotide arrays, have emerged as the principal platforms for performing genome-wide diversity analysis. They have wide-ranging potential applications including comparative genomics, polymorphism discovery and genotyping. The identification of inheritable genetic markers also permits the analysis of quantitative traits, population studies and linkage analysis. In this review, we will discuss the application of oligonucleotide arrays, in particular high-density oligonucleotide arrays for elucidating genetic diversity and highlight some of the directions that the field may take.