Objectives: The incidence of infant allergic diseases have increased recently, and it may be caused by multiple influences of both genetic and environmental factors from the fetal stage through infancy. In this study, we analyzed a data subset from the South Kyushu and Okinawa (SKO) Study Area of Japan Environment and Children’s Study (JECS) to determine the relationship of allergic diseases in infants with mothers’ characteristics and/or infants’ life habits, especially sleeping. Methods: A total of 3873 mother-infant pairs from the SKO Regional Center of JECS were included. The mothers responded to questionnaires in the first trimester of their pregnancy and the self-reported questionnaire when their infants were 1 year old. Student’s t-test, chi-square test, trend test, and logistic regression analysis were carried out to analyze the associations between the infants’ allergic diseases and the mothers’ genetic characteristics and/or sleeping habits of infants. Results: Maternal allergic diseases were significantly associated with increased infant allergy risk (OR: 1.93, 95% CI: 1.63–2.27). The number of allergic diseases of mothers was also significantly associated with infant allergy, and the trend test showed an increasing risk of infant allergy (p<0.001). Regarding infants’ life habits, the infants who sleep in the prone position had a higher allergic disease risk than those who sleep in other positions (OR: 1.46, 95% CI: 1.17–1.83). These significant associations were observed regardless of the presence of allergy in mothers. Conclusions: This study suggests that the development of allergic diseases in infants may be caused by the multiple participation of both genetic and environmental factors.