Micronutrient malnutrition, particularly deficiencies in iron and zinc, are the major nutritional problems common in rice-consuming countries. The cost of these deficiencies in terms of lives lost and quality of life is vast. Since rice is the staple food for more than half of the world’s population even a small increase in its nutritive value would be highly beneficial for human health. Several strategies including supplementation and fortification programs are continuing to address this problem. Recently, breeding staples with high micronutrient content dubbed ‘biofortification’ has evolved as a new strategy to address micronutrient malnutrition. To accelerate the development of elite lines with increased micronutrient content, the understanding of the genetic basis is the prerequisites for manipulation of these micronutrients. Several DH populations were developed from the crosses between popular indica varieties of the target environments and japonica donor cultivars. Four DH populations were field evaluated in replicated yield trials for three seasons at farm station, IRRI and grain zinc and iron data were generated through inductively coupled mass spectrometry. The set of four DH populations was genotyped using SSR markers. The current status of QTL mapping would be presented.