Deletion line-based high-density physical maps revealed that the wheat (Triticum aestivum) genome is partitioned into gene-rich and -poor compartments. Available deletion lines have bracketed the gene-containing regions to about 10% of the genome. Emerging sequence data suggest that these may further be partitioned into "mini" gene-rich and gene-poor regions. An average of about 10% of each gene-rich region seem to contain genes. Sequence analyses in various species suggest that uneven distribution of genes may be a characteristic of all grasses and perhaps all higher organisms. Comparison of the physical maps with genetic linkage maps showed that recombination in wheat and barley (Hordeum vulgare) is confined to the gene-containing regions. Number of genes, gene density, and the extent of recombination vary greatly among the gene-rich regions. The gene order, relative region size, and recombination are highly conserved within the tribe Triticeae and moderately conserved within the family. Gene-poor regions are composed of retrotransposon-like non-transcribing repeats and pseudogenes. Direct comparisons of orthologous regions indicated that gene density in wheat is about one-half compared with rice (Oryza sativa). Genome size difference between wheat and rice is, therefore, mainly because of amplification of the gene-poor regions. Presence of species-, genera-, and family-specific repeats reveal a repeated invasion of the genomes by different retrotransposons over time. Preferential transposition to adjacent locations and presence of vital genes flanking a gene-rich region may have restricted retrotransposon amplification to gene-poor regions, resulting into tandem blocks of non-transcribing repeats. Insertional inactivation by adjoining retro-elements and selection seem to have played a major role in stabilizing genomes.