Background and Objective The association between periodontal disease and nutrient intake was examined using linked data from the 2005 National Health and Nutrition Survey, the Comprehensive Survey of Living Conditions and the Survey of Dental Diseases from the same year ‘using linked data from the National Health and Nutrition Survey, the Comprehensive Survey of Living Conditions and the Survey of Dental Diseases, all from 2005’. There has been increasing focus on the importance of nutritional factors in disease in recent years, but very few studies in Japan have looked at the association between periodontal disease and nutrients. Therefore, in the present study we investigated factors associated with periodontal disease, particularly in terms of nutrient intake. Material and Methods Data from 3043 individuals, ≥ 20 years of age (the original study sample comprised 4873 individuals, but those younger than 20 years of age and pregnant women were excluded from the present study) were compiled from linked responses to these three surveys from the same year. Permission to use the data was obtained from the Lifestyle‐Related Diseases Control General Affairs Division of the Ministry of Health, Labor, and Welfare, Japan. Information including basic attributes, family structure, economic status, physical condition, lifestyle habits, diet, dental habits, blood data, intake of foods (including the categories of food) and nutrient‐related information were obtained from the linked data. The individual maximum Community Periodontal Index (CPI) was used as an index of periodontal disease. Subjects were divided, according to maximum CPI, into groups in which CPI = 0–2 or CPI = 3–4, and associations between CPI and basic attributes, family structure, economic status, physical condition, lifestyle habits, diet, blood data and food intake were analyzed. Results Multivariate analysis revealed that the percentage of calories from fat was a nutrient factor associated with periodontal disease, with the percentage of calories from fat being significantly lower in the group with advanced periodontal disease. Conclusion The results suggest that a low‐fat, high‐carbohydrate diet is related to periodontal disease. A more detailed analysis of this topic will be conducted in the future using different indices of periodontal disease.