Early organogenesis represents a key step in animal development, where pluripotent cells diversify to initiate organ formation. Here, we sampled 300,000 single cell transcriptomes from mouse embryos between E8.5 and E9.5 in 6-hour intervals and combined this new dataset with our previous atlas (E6.5-E8.5) to produce a densely sampled time course of >400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction identified complex waves of blood and endothelial development, including a new programme for somite-derived endothelium. We also dissected the E7.5 primitive streak into four adjacent regions, performed scRNA-Seq and predicted cell fates computationally. Finally, we defined developmental state/fate relationships by combining orthotopic grafting, microscopic analysis and scRNA-Seq to transcriptionally determine cell fates of grafted primitive streak regions after 24h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with computationally predicted fates, demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in developmental biology and guide the in vitro production of cells for organ regeneration and repair.