Purpose: The aim of this study was to investigate the association of masticatory ability and dental status with intake of fruits and vegetables after adjusting for other factors in independently living elderly Japanese subjects. Materials and Methods: The study population consisted of 1,535 community-dwelling, independent elderly subjects over the age of 60 years. Self-assessed general health, financial status, dental status, self-assessed masticatory ability by food acceptance, and frequency of food intake were evaluated from responses to a questionnaire. Multiple logistic regression analysis for shortage of food intake was carried out. Results: Of the participants, 29% had natural dentitions in both the maxilla and mandible and 15% were edentulous in at least one arch and wearing a complete denture. Percentages of participants with nutrient shortages of meat, fish and seafood, green and yellow vegetables, other vegetables, and fruits were 44%, 17%, 30%, 33%, and 12%, respectively. Multiple logistic regression analysis showed that men and subjects with a poor financial status had significant associations with shortages of dietary intake. In addition, shortages of meat, green and yellow vegetables, other vegetables, and fruit were significantly related to poor masticatory ability but not to dental status. Masticatory ability was significantly associated with shortages of green and yellow vegetables. Conclusion: Multivariate analyses showed that after adjusting for age, sex, and financial status, self-assessed masticatory ability rather than dental status by itself was significantly associated with shortages in vegetable and fruit intake in independently living elderly Japanese subjects.