The goals of our study were to analyze change of global gene expression profile of mouse blastocysts after slow-freezing and to explore molecular mechanism underlying the decreased pregnancy rate caused by cryopreservation. The results showed that superovulation differentially regulated the expression of 288 genes with at least 2.0-fold change considerations. Among which, 275 genes were down-regulated and the remainder up-regulated in the cryopreserved group. The independent analysis with real-time PCR fully confirmed the results of microarray. These differential genes were classified into eighteen functional groups belonging to biological process, molecular function, and cellular component. Twenty nine genes could be categorized into one or more of KEGG pathways. The pathways of mitogen-activated protein kinase, Wnt and cell cycle were the most predominantly affected. Thus, the expression pattern reflected a broad spectrum of consequences of slow-freezing on the blastocysts, with most effects on stress-related and cell cycle-related genes.