A network of molecular interactions between genes and proteins drives animal embryonic development, but much less is known about the role of endogenous low molecular weight metabolites in the early developing embryo. Using liquid chromatography/mass spectrometry (LC-MS), a metabolic fingerprinting analysis is conducted to discover if significant changes in the endogenous cellular metabolites occur between different embryonic stages of development prior to organ formation from the early blastula until the young pharyngula. Principal component analysis (PCA) shows that the developmental stages of the zebrafish are metabolically distinct, and reproducibly describes the temporal changes in the metabolome of the different embryonic stages. Clustering analysis finds several main classes of regulation, namely, a constant increase, a constant decrease, and an up-down regulation. The observations show that the early zebrafish metabolome is very dynamic and stage-specific, and that endogenous metabolites are developmentally regulated to a much stronger degree than anticipated.