Understanding cell fate patterning and morphogenesis in the mammalian embryo remains a formidable challenge. Recently, in vivo models based on embryonic stem cells (ESCs) have emerged as complementary methods to quantitatively dissect the physical and molecular processes that shape the embryo. Here we review recent developments in using ESCs to create both two- and three-dimensional culture models that shed light on mammalian gastrulation. © 2018 Elsevier Inc.