A method and system of in vitro developmental toxicity testing comprising the steps of micropatterning an extracellular matrix; growing embryonic stem cells on the micropatterned extracellular matrix in the presence of mesoendodermal induction and testing for change of the geometrical mesoendoderm structure in the presence or absence of a test compound wherein (1) a decrease in mesoendodermal differentiation and/or (2) a change in morphology of the geometrical mesoendoderm structure in the presence of the test compound compared to cells in the absence of the test compound indicates that the test compound is a developmental toxic agent.