Objective Obesity associated with an increased consumption of ultra-processed foods (UPF) has been reported by studies abroad using the NOVA food classification system, an international framework for classifying food according to the degree of processing. However, no such study has been conducted in Japan. In this study, we evaluated the association between UPF consumption, nutrient intake, and obesity using the NOVA system.Method In September 2017, we conducted a survey using a questionnaire of patients who had attended routine health checkups in Manazuru Town, Kanagawa Prefecture and collected their three-day dietary records as well as medical examination results. The final analysis included 169 patients (66 men, 103 women). Food consumed by the respondents were classified into four groups of NOVA systems. The dietary share of UPF (UPF energy ratio) was compared to total energy intake (except alcoholic beverages and eating out). Nutrient intake and obesity risk were compared across the UPF energy ratio tertile (low, middle, and high intake). Covariance and logistic regression analysis were conducted and adjusted based on age, sex, household structure, education, income, and total energy intake (except energy-providing nutrients, macronutrients, and protein intake per body weight) to analyze the association between UPF consumption and nutrient intake. Finally, for obesity, we adjusted for physical activity and smoking status using a similar analysis of the relationship between UPF consumption and energy providing nutrients and macronutrients.Result Approximately 75% of patients investigated were older than 65 years. The average (standard deviation) UPF energy ratio was 29.7% (15.0). There were no significant differences in socioeconomic status among groups according to the UPF energy ratio. The high-UPF group had a significantly greater total energy intake. However, the protein energy ratio, protein intake per body weight, dietary fiber, and vitamins A, E, K, B 1 , B 6 , C, niacin, folic acid, potassium, magnesium, and iron intake were significantly lower in the high-UPF group. Moreover, the high-UPF group had a significantly higher BMI. The odds ratio for obesity was higher (4.51[1.50-13.57]) in the high-UPF group than in the low-UPF group (1.00).Conclusion Those who consumed more UPF had lower protein intake and suffered from multiple vitamin and mineral deficiencies. Furthermore, their energy intake was greater, and the odds ratio for obesity was significantly higher. It has been suggested that excessive UPF consumption warrants further attention.