Silicon in rice has been demonstrated to be involved in resistance to lodging, tolerance to both drought and salinity, and also enhances resistance to pests and diseases. The aim of this study was to determine the range of silicon content in a set of rice (Oryza sativa L.) accessions, and to determine if the natural variation of shoot silicon is linked to the previously identified silicon transporters (Lsi genes). Silicon content was determined in 50 field-grown accessions, representing all sub-populations of rice, with all accessions being genotyped with 700K SNPs. SNPs within 10 kb of the Lsi genes were examined to determine if any were significantly linked with the phenotypic variation. An XRF method of silicon determination compared favourably with digestion and colorimetric analysis. There were significant genotypic differences in shoot silicon ranging from 16.5 – 42.4 mg g-1 of plant dry weight, there was no significant difference between the rice sub-populations. Plants with different alleles for SNPs representing Lsi2 and Lsi3 were significantly different for shoot silicon content. Shoot silicon correlated negatively with grain arsenic in the tropical and temperate japonica sub-population, suggesting that accessions with high shoot silicon have reduced grain arsenic. This study indicates that alleles for Lsi genes are excellent candidate genes for further study to explain the natural variation of shoot silicon in rice.