Objective Children are not little adults. Such a statement summarises the growing interest in the role of prenatal and early-life exposure to environmental factors and the development of adverse health effects. NewGeneris is a multidisciplinary research project conducted within the European Union in the food quality and safety area of the sixth framework programme. The specific hypothesis to be tested within NewGeneris is that maternal exposure to dietary compounds (ie, polycyclic aromatic hydrocarbons, heterocyclic amines, nitrosamines, acrylamide, the mycotoxin deoxyvalenol and TCDD-PCB, alcohol, DNA reactive aldehydes) results in in utero exposure and in molecular events in the unborn child leading to increased risks of cancer and immune disorders in later childhood.

Methods European mother and child cohorts have been identified as base populations for the recruitment of pregnant women. Food frequency questionnaires and biomarkers (measured in blood samples collected from mother–child pairs) are used to measure exposure, individual susceptibility to toxic agents, early biological effects including omics’ based signatures.

Results Research procedures were developed and validated through the conduct of early pilot studies nested within the collaborative research and included in the research protocol. The protocol specifically accounts for factors that may affect the level of biomarkers such as processing of biological samples, time to processing and to assay and assay methodology.

Conclusions Specific issues in planning and undertaking a multicentre study are discussed, including the sample size required to test the study main hypothesis and the statistical plan and ethical considerations concerning transboundary exchange of human samples and data.