The animal embryo is a self-organizing entity. At the start of gastrulation, mammalian embryos are made of a single layer of cells. Extensive cell rearrangements coupled with position-dependent cell differentiation patterns this layer to form the blueprint for the animal body. The early steps patterning the mammalian embryo are poorly understood. Our laboratory has contributed to understanding how the mesoderm germ layer is patterned along the anterior-posterior axis. Earlier we showed that the inhibition of two major signaling pathways, Wnt and Nodal, instructs the anterior mesoderm to become the progenitors of heart and head muscles. Our current work, using chemical and genetic manipulation of embryo organoid models, shows that preclusion of retinoic acid signaling is key to specify the identity of the anterior mesoderm. We also find central roles for T-box transcription factors, Eomes and Tbxt, in anterior mesoderm fate specification, by suppressing posterior identity. In the context of left-right patterning, our work reveals the function of another T-box factor, Tbx6, in initiating the bilateral symmetry breaking mechanism. Using mouse genetics and genome-wide binding site analysis, our research shows that Tbx6 controls the left-right patterning mechanism at multiple critical regulatory steps. These findings address major knowledge gaps in the field and help us understand the early patterning mechanisms laying down the animal body plan.