Vitamin E and phytosterols are both valuable nutrients that act as antioxidants in human bodies. Understanding the genetic basis of these traits is necessary for the improvement of nutritional quality by breeding. In this study, 119 rice accessions of diverse origin were genotyped using 232 SSR markers to identify marker–trait associations with Vitamin E and phytosterols in rice. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r2 value for all intra-chromosomal loci pairs was 0.3361. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 81 marker–trait associations were identified using 232 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping. The results from this association mapping study will be the basis for improving rice nutritional quality.