The BABY1000 birth cohort study aims primarily to identify modifiable risks prior to and during pregnancy that impact lifelong health, particularly intergenerational obesity. By extending from preconception or early pregnancy and including comprehensive data collection at multiple timepoints throughout the first 1000 days of life, BABY1000 informs potential intervention studies of environmental exposures (particularly very early in the perinatal period) and associated health outcomes. Women were enrolled when planning pregnancy or at 12 weeks’ gestation, with follow-up extending to the child’s second birthday. Participants were primarily recruited at existing preconception and antenatal clinics from the Royal Prince Alfred Hospital (RPAH) in Sydney, Australia. The mean age of BABY1000 mothers at baseline was 33.3 years.