Background: Cell polarity is essential for directed migration of mesenchymal cells and morphogenesis of epithelial tissues. Studies in cultured cells indicate that a condensed Golgi Complex (GC) is essential for directed protein trafficking to establish cell polarity underlying directed cell migration. Dynamic changes of the GC intracellular organization during early vertebrate development remain to be investigated. Results: We used antibody labeling and fusion proteins in vivo to study the organization and intracellular placement of the GC during early zebrafish embryogenesis. We found that the GC was dispersed into several puncta containing cis- and trans-Golgi Complex proteins, presumably ministacks, until the end of the gastrula period. By early segmentation stages, the GC condensed in cells of the notochord, adaxial mesoderm, and neural plate, and its intracellular position became markedly polarized away from borders between these tissues. Conclusions: We find that GC is dispersed in early zebrafish cells, even when cells are engaged in massive gastrulation movements. The GC accumulates into patches in a stage and cell-type specific manner, and becomes polarized away from borders between the embryonic tissues. With respect to tissue borders, intracellular GC polarity in notochord is independent of mature apical/basal polarity, Wnt/PCP, or signals from adaxial mesoderm. Developmental Dynamics 245:678-691, 2016. Key findings: Golgi Complex is dispersed into multiple bodies in the gastrulating vertebrate zebrafish, implying a compact morphology is not required for polarized cell movement. Golgi Complex condenses into single or few bodies in cells of the notochord and somites by early segmentation stages. Golgi Complex becomes localized within cells so that it lies away from the exterior of the notochord or somites. Intracellular polarization of Golgi Complex does not depend on Wnt/Planar Cell Polarity signaling or signals originating in the adaxial mesoderm.