The relationship between food avoidance during infancy and the growth of Japanese infants in a community health setting has not been well evaluated. In order to assess the growth of infants who avoided either of the three major allergen foods in Japan, eggs, milk or wheat, we employed the results of 4 physical checkups recorded in maternity passbooks and administrated a questionnaire on allergic diseases, height and weight at birth to the guardians of 1,132 infants at the age of 3.5 years. Data was obtained from 890 subjects (78.6%) and 662 subjects (58.5%) who met the inclusion criteria were analyzed. The height, weight and body mass index percentile scores of each subject were calculated. Subjects who avoided either of the three foods at 3.5 years had lower weight percentile scores at 1.5 years, lower height and weight percentile scores at 3.5 years, and lower weight growth rates, compared with the subjects who did not avoid any of the three foods at 3.5 years (P=0.02, 0.03, 0.03, 0.01). The results suggested that there was a negative relationship between physique and food avoidance in infants, and that physical and nutritional assessments are important for food avoiders.