Recent advances in whole genome sequencing have allowed identification of genes for disease susceptibility in humans. The objective of our research was to exploit whole genome sequences of 13 rice inbred lines to identify variants and candidate genes for resistance to sheath blight, a disease of worldwide significance. Whole genome sequencing by the Illumina GA II platform across all lines produced an average 5X coverage with ~ 700 K variants detected per line when compared to the Nipponbare reference genome. Variants were found in 11 of 12 chromosomes.  A “common variant” and a statistical biplot filtering strategy were utilized to identify non-synonymous SNPs (nsSNPs) between two groups of known resistant and susceptible lines.  A total of 324 nsSNPs detected in the resistant lines were absent in the susceptible group.  More than 200 genes containing the selected nsSNPs were grouped into 42 categories based on gene family / gene ontology.  Several candidate resistance genes belonged to families reported in previous studies, and a few novel candidates were also identified.  A subset of 25 nsSNPs detected in 24 genes was selected for further study. All nsSNPs in this subset were found in dbSNP.  Individual alleles of the 25 nsSNPs were evaluated by PCR whose presence or absence corresponded to known resistant or susceptible phenotypes of 12 additional lines. To date Sanger sequencing has confirmed presence of 12 nsSNPs in two lines.