Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridizationof two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed thesequence of five duplicated regions from different chromosomal locations. We also compared corresponding regionsfrom sorghum and rice, two important crops that have largely collinear maps with maize. The split of sorghum andmaize progenitors was recently estimated to be 11.9 Mya, whereas rice diverged from the common ancestor of maizeand sorghum ∼50 Mya. A data set of roughly 4 Mb yielded 206 predicted genes from the three species, excludingany transposon-related genes, but including eight gene remnants. On average, 14% of the genes within the alignedregions are noncollinear between any two species. However, scoring each maize region separately, the set ofnoncollinear genes between all four regions jumps to 68%. This is largely because at least 50% of the duplicatedgenes from the two progenitors of maize have been lost over a very short period of time, possibly as short as 5million years. Using the nearly completed rice sequence, we found noncollinear genes in other chromosomalpositions, frequently in more than one. This demonstrates that many genes in these species have moved to newchromosomal locations in the last 50 million years or less, most as single gene events that did not dramatically altergene structure.