The acquisition of mineral elements from the soil and their distribution within plant tissues are important physiological and biochemical processes essential for plant growth and development. Cereals such as rice (Oryza sativa) are also an important dietary source of both the essential micronutrients (e.g. iron and zinc) and the toxic trace elements (e.g. cadmium and arsenic) to humans. The genetic basis underlying the natural variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at approximately 6.4 million SNP loci. We identified 72 loci associated with natural ionomic variations, including 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum and Grain Number, Plant Height, and Heading Date 7 for nitrogen. Comparison of GWAS data from rice vs. Arabidopsis thaliana also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.