Developmental design principles organize heterogeneous cell populations with systems-level accuracy and autonomy – manifesting the precise form and function of adult organs. Our digestive organ, the coiled, multi-layered small intestine, arises from the dramatic transformation of a linear gut tube of homogenous cells. In my dissertation research, I have applied multi-disciplinary approaches to reveal how mesenchymal cells in the developing gut contribute to building and maintaining the sophisticated architecture of the mammalian intestine at the molecular, cellular, mechanical, and metabolic levels. An evolutionarily conserved counterclockwise rotation of the embryonic gut tube is critical for generating the twisted form of the small intestine. Malrotation can strangulate the gut’s blood supply – a pediatric emergency called midgut volvulus. In Chapter II of this dissertation, I discovered that asymmetrical developmental signals amplify the left-determining transcription factor PITX2 to set up accelerator-brake mechanical feedback across the left-right axis of gut mesenchymal cells for robust control of gut rotation. Combing classical and modern approaches to chicken embryology and mouse genetics, I measured and manipulated signal transmission, gene expression, and mechanical properties of the early embryonic gut to show how developmental programs can pattern tissue stiffness to make complex organ shapes. Collectively, these findings redefine a long-standing dogma of how visceral organs interpret the embryonic body plan to execute local programs of asymmetry – combining biomechanical and biochemical inputs. This study opens new paths to understanding how laterality information is inputted into the organismal body plan. Further in development, the gut mesenchyme is rearranged and differentiated to pattern smooth muscles along the gut wall and villus stroma for intestinal contractile activity. In Chapter III of my dissertation, I built a comprehensive map of intestinal cell developmental trajectories using single-cell transcriptomics and in vivo, quantitative lineage tracing. Using these trajectories, I discovered a developmental progenitor/adult stem cell state within the intestinal mesenchyme that is responsible for assembling villus smooth muscles at birth and their self-renewal during adult intestinal homeostasis. I found that these progenitors enable the assembly of muscles around the specialized lymphatic capillaries called lacteals, whose constriction is crucial to the uptake of dietary fats into systemic blood circulation. Structural defects in this fat absorption apparatus arising by perturbing their contact-dependent signaling resulted in reduced efficiency of fat absorption. These studies reveal the origin, assembly, and regenerative mechanism of the intestinal fat-absorption apparatus and progenitor cell states which can be targeted to accelerate intestinal recovery after disease. Studies have long debated the origin of the intestinal lymphatic system and its specialized structures and functions. However, the plasticity of endothelial progenitors during development has prevented researchers from reconstructing organotypic lymphatic networks. In Chapter IV of my dissertation (manuscript in preparation), I applied single-cell analyses and in vivo staining and quantitative lineage tracing experiments of bona fide endothelial progenitor-restricted markers to identify the origin of intestinal lymphatics and built tools for delineation of their function. In Chapters V, VI, and VII I present published book chapters and papers detailing classical and modern methods for in vivo genetic, pharmacological, and surgical manipulation of the embryonic gut mesenchyme using the chicken embryo model. Altogether, my studies reveal concerted and highly localized mesenchymal cell behaviors and molecular mechanisms responsible for the coiled structure and fat absorption function of the vertebrate intestine. Moreover, the tools, datasets, and protocols I have developed serve as critical resources for understanding and manipulating intestinal cell heterogeneity.