The goal of the Japan Environment and Children’s Study (JECS) is to improve the health and welfare of children and to contribute to better risk management of chemical substances in the environment. The study will examine hypotheses related to reproduction, congenital anomalies, neuropsychiatric development, immunity, metabolism and endocrine system. The hypotheses will be tested for indicative outcomes in combination with exposure to chemicals, as well as confounders and modulators, such as chemical, physical, genetic, social and lifestyle-related factors. A total of 100,000 pregnant women associated with the selected study locations were recruited during the first three years starting January 2011. Their children will be followed up until the age of 13 years. The main study (nationwide survey) will include all participants recruited in all regional centres. Substudies will be conducted on randomly selected individuals from among all the participants. In the main and substudies, blood, urine, hair and breast milk samples will be collected from mothers. Blood, hair, and urine samples as well as umbilical cord blood at delivery will be collected from the children. Blood samples will also be collected from fathers. Each specimen will be analysed for specific chemical substances. In addition, genetic background will be evaluated. The collected blood samples for genetic assessments will be stored at the national centre. The detailed assessment procedures will be reviewed for approval by IRBs.