In this review, we present an initial plan for exposure assessment in the Japan Environment and Children’s Study (JECS) by focusing on a biomonitoring technique and discuss the challenges encountered when using the biomonitoring technique for exposure measurements. JECS registered 103,099 pregnant mothers and has been following children born to them. Various biological samples were collected from mothers during pregnancy (blood and urine), at birth (blood and hair) and at check-up one month after birth (breast milk). Samples were also collected from children at birth (cord blood) and at check-up one month after birth (hair and blood spot). Those samples will be used to assess maternal and foetal exposures to chemical substances. Measurement reliability, i.e., intraclass correlation coefficient (ICC), and attenuation bias related to low ICCs should be taken into consideration when using the biomonitoring results. Along with the biomonitoring technique, simulation models, pharmacokinetic (PK) models and exposomics techniques are under development in JECS. New analytical techniques include deciduous teeth measurements and -omics analyses. In particular, PK models and sensor technologies are one of the most important methodologies for future JECS exposure analyses. Statistical methods for examining the effects of intercorrelated multiple exposures as well as nondetection data should also be explored.