Using the CD-1 mouse conceptus, we investigated gene expression changes found in vivo from gestational day 8 (GD) through GD9 at 6 h intervals, and then at 24 h intervals through GD11. Data sets were analyzed for patterns in transcriptional expression over a time course as well as to compare the GD9 in vivo mouse conceptus with conceptuses cultured for 24 h from GD8 in whole embryo culture (WEC). Our results show that during development from GD8 to GD11, a series of metabolic pathways related to carbohydrate metabolism and energy production, as well as the signal transduction pathways of the MAPK cascade and Wnt signaling were changing. Previous results have shown that WEC successfully sustains morphological development comparable to that in vivo for at least 24 h. We report here that, in the absence of morphological malformations following 24 h WEC, 329 genes were differentially expressed between in vivo and in vitro developing conceptuses.