The release of the Triticum aestivum Chinese Spring (CS) RefSeq v1.0 genome, enabled us to develop DAWN (Diversity Among Wheat geNomes), a tool that allows visualization of genetic diversity in a genome context. DAWN enables researchers and breeders alike to investigate genotypic differences between wheat lines on the level of whole chromosomes down to individual genes. With DAWN we are now able to visualize small and large chromosomal deletions, we can identify haplotypes at a glance and we can spot consequences of selective breeding. For instance, DAWN allows us to detect the breakpoints of alien introgression segments brought into an elite line when transferring desired genes. Furthermore, we can find possible explanations for reduced recombination in parts of a chromosome, we can predict regions with linkage drag, and specifically look at diversity in pericentromeric regions. DAWN integrates public genomic data from 16 accessions with the full genome assembly of CS and also with gene expression data, probe locations of various molecular marker platforms (Axiom 820K, 90K iSelect, DArT and SSR) and EST information. Thus, researchers and breeders have the tools to relate the information available in DAWN to their own germplasm pools and genetic maps.