The last 20 years has seen a tremendous growth in molecular genetics research and breeding rice. While there have been some outstanding successful examples of rice molecular breeding, there have also been many failures. Careful analysis of successes and failures indicates several critical factors including parameters of the quantitative trait loci (QTL) mapping experiment and subsequent testing which is referred to as QTL and marker validation. In rice, validation research is seldom reported and more activities are needed, as has been done in other cereals. In order to leverage the wealth of publicly-available genomics resources in rice for molecular breeding in the future, breeders will need: carefully planned and well-executed QTL mapping experiments, QTL and marker validation activities, efficient genotyping systems and processes, cheaper genotyping systems and more breeder-friendly analytical tools. It is imperative that future activities focus on bridging the disconnection between breeders and molecular geneticists and achieving improved co-ordination and collaboration. Arguably, the highest priority to achieve success and synergy regarding varietal/germplasm development in the short-term and the future is the need to integrate breeding with molecular genetics research.