We describe a system that permits the automated analysis of reporter gene expression in Caenorhabditis elegans with cellular resolution continuously during embryogenesis. We demonstrate its utility by defining the expression patterns of reporters for several embryonically expressed transcription factors. The invariant cell lineage permits the automated alignment of multiple expression profiles, allowing direct comparison of the expression of different genes' reporters. We also used this system to monitor perturbations to normal development involving changes both in cell-division timing and in cell fate. Systematic application of this system could reveal the gene activity of each cell throughout development.