Analysis of the protein complement of a biological system through proteomics provides the opportunity to directly monitor the functional readout of gene expression. In this study, proteomics was applied to the mouse embryo to investigate the molecular events underlying the processes occurring at the stage of neural tube closure. Protein profiles of embryos between embryonic days 8.5 and 10.5 exhibited a number of stage-specific changes. Identification of developmentally regulated proteins by mass spectrometry revealed several groups of functionally related proteins including circulatory, cytoskeletal, and stress proteins. Additional proteins of unknown function were identified, such as Copine 1 and PICOT, whose developmental regulation was previously unsuspected.