Background: Retrospective studies suggest that maternal exposure to a severe stressor during pregnancy increases the fetus' risk for a variety of disorders in adulthood. Animal studies testing the fetal programming hypothesis find that maternal glucocorticoids pass through the placenta and alter fetal brain development, particularly the hypothalamic-pituitary-adrenal axis. However, there are no prospective studies of pregnant women exposed to a sudden-onset independent stressor that elucidate the biopsychosocial mechanisms responsible for the wide variety of consequences of prenatal stress seen in human offspring. The aim of the QF2011 Queensland Flood Study is to fill this gap, and to test the buffering effects of Midwifery Group Practice, a form of continuity of maternity care. Methods/design: In January 2011 Queensland, Australia had its worst flooding in 30 years. Simultaneously, researchers in Brisbane were collecting psychosocial data on pregnant women for a randomized control trial (the M@NGO Trial) comparing Midwifery Group Practice to standard care. We invited these and other pregnant women to participate in a prospective, longitudinal study of the effects of prenatal maternal stress from the floods on maternal, perinatal and early childhood outcomes. Data collection included assessment of objective hardship and subjective distress from the floods at recruitment and again 12 months post-flood. Biological samples included maternal bloods at 36 weeks pregnancy, umbilical cord, cord blood, and placental tissues at birth. Questionnaires assessing maternal and child outcomes were sent to women at 6 weeks and 6 months postpartum. The protocol includes assessments at 16 months, 2 1/2 and 4 years. Outcomes include maternal psychopathology, and the child's cognitive, behavioral, motor and physical development. Additional biological samples include maternal and child DNA, as well as child testosterone, diurnal and reactive cortisol. Discussion: This prenatal stress study is the first of its kind, and will fill important gaps in the literature. Analyses will determine the extent to which flood exposure influences the maternal biological stress response which may then affect the maternal-placental-fetal axis at the biological, biochemical, and molecular levels, altering fetal development and influencing outcomes in the offspring. The role of Midwifery Group Practice in moderating effects of maternal stress will be tested.