Recent studies in certain crop species have identified extensive genomic variation when evaluating diverse germplasm with different gene array and sequencing technologies. The objective of our research was to assess genomic variation of 13 elite rice (Oryza sativa L.) inbred varieties by whole genome sequencing (WGS). A total of 1.3 M non-redundant variants were detected with SNP frequencies being nearly equal for O. sativa spp. indica vs. O. sativa spp. japonica varieties. The largest proportion of SNPs was found in intergenic regions while frequency of insertion/deletions (indel) variants was rare. Measures of overall subpopulation differentiation and SNP diversity were relatively high, punctuated by specific chromosomal regions that featured either extremely low or high levels of variation. Only a small percentage of SNPs fixed in the indica varieties were absent in the japonica varieties. Both phylogenetic and GGE-biplot analyses based on sharing or frequency of alleles revealed that the 13 varieties could be assigned to three distinct groups. Genome-wide linkage disequilibrium in general extended up to 1 Mb, but substantial variation was observed within each chromosome. Results from this study indicate that considerable genomic variation occurs even among elite inbred rice varieties that can be exploited in future crop improvement efforts. WGS of elite material increases our understanding of rice diversity at high sequence resolution that complements previous research with diverse germplasm and different sequencing strategies.