Miniature inverted-repeat transposable elements (MITEs) are ubiquitous in high eukaryotic genomes. More than 178,000 MITE sequences of 338 families are present in the genome of rice (Oryza sativa) cultivar Nipponbare. Interestingly, only two of the 338 MITE families have homologous sequences in the genome of Brachypodium distachyon, a relative in the grass family. Therefore, the vast majority of MITEs in the rice genome were originated and amplified after the divergence of Oryza and Brachypodium. Comparison between rice cultivar Nipponbare and another rice cultivar 93-11 showed 14.8% of MITEs exhibit presence/absence (P/A) polymorphism. The P/A polymorphism was mainly attributed to recent MITE transpositions, while less than 10% of the P/A polymorphism was caused by MITE excisions. Therefore, the high P/A polymorphisms of MITEs may generate considerable gene expression and phenotypic diversity for O. sativa.