Improved understanding of the mechanism behind periodontal tissue destruction, the potential protective role of nutrients and the advent of modern genomic measurement tools has led to an increased interest in the association between nutrition and periodontal disease. To date, evidence for a direct link between periodontal disease and nutrition has come mainly from large observational cross-sectional studies or very small double-blind randomized supplementation trials, with a large proportion finding no significant association between the nutrient being analyzed and markers of periodontal disease status. The advent of the ‘genomic era’ has introduced the concept of nutrigenomic studies, which aim to reveal the relationship between nutrition and the genome to provide a scientific basis for improved public health through dietary means. Used alongside relatively inexpensive high-throughput technology, this will allow the effect of diet on the etiology of periodontal disease to be studied in greater detail. As it is extremely likely that interactions between genotype and diet are important in determining the risk of the most common complex diseases, it is highly probable that these interactions will be important in determining periodontal disease risk. Numerous nutritional genetic studies where the outcome measures have been markers of disease risk, most notably cardiovascular disease and cancer, provide proof of principle, highlight the importance of understanding these interactions and illustrate where the effect of dietary modification on periodontal disease progression may have been overlooked previously by observational studies.