This supplement presents some of the methodological issues that arose during the early phases of protocol development for the National Children's Study (NCS), a probability sample of 100,000 children that will be followed prospectively from pregnancy through 21 years of age, and to share some of the challenges and solutions that were discussed. These papers on motor, social/emotional, psychiatric and neurocognitive/behavioural development do not define the protocol of the NCS, but reflect methodology related to the design of research and assessment of developmental trajectories in children that may be useful to other epidemiologists planning similar longitudinal studies.