Is the information currently available to adjust nutritional recommendations and develop individualized nutrition? No. There is not even the information needed for setting dietary recommendations with confidence now at the group level. Will it be available soon? The answer to this question depends on the drive and will of the nutritional community, the success in recruiting funding to the area, the education of nutritionists and the spawning of great ideas and approaches. The emerging tools of genomics, proteomics and metabolomics are enabling the in-depth study of relationships between diet, genetics and metabolism. The advent of technologies can be compared with the discovery of the microscope and the new dimensions of scientific visualization enabled by that discovery. Nutritionists stand at the crest of new waves of data that can be generated, and new methods for their digestion will be required. To date, the study of dietary requirements has been based largely on a black box approach. Subjects are supplemented or depleted and clinical outcomes are observed. Few recommendations are based on metabolic outcomes. Metabolomics and nutrigenomics promise tools with which recommendations can be refined to meet individual requirements and the potential of individualized nutrition can be explored. As yet, these tools are not being widely applied in nutritional research and are rarely being applied by nutritionists. The result is often interesting research that is frequently nutritionally flawed, resulting in inappropriate conclusions. Nutritional education is needed to put nutritionists at the forefront of the development of applications for these technologies, creating a generation of nutrigenomicists. A new generation of nutritionists should be working interdisciplinarily with geneticists, molecular biologists and bioinformaticians in the development of research strategies. The present paper reviews the current status of nutrigenomic research, the current controversies and limitations, and developments needed to advance nutrigenomics and explore fully the promise of individualized nutritional recommendations.