In vitro maturation (IVM) of mammalian oocytes does not support the same rates of embryo development or pregnancy when compared to oocytes that have matured in vivo. Therefore, environment has a significant influence on the oocyte's ability to complete maturation and acquire the mRNA and proteins required for successful fertilization and normal embryonic development. The aim of this study was to analyze the MII oocyte transcriptome between in vivo and in vitro conditions. Total RNA was extracted, processed and hybridized to the Affymetrix GeneChip Bovine Genome Array. Following normalization of the microarray data, analysis revealed 10 differentially expressed genes after IVM compared to in vivo matured controls, including Aqp3, Sept7, Abhd4 and Siah2 (P<0.05). K-means cluster analysis coupled with associated gene ontology, identified several biological processes affected by IVM, including metabolism, energy pathways, cell organization and biogenesis, and cell growth and maintenance. Quantitative real-time PCR validated the microarray data and also revealed altered expression levels after IVM of specific putatively imprinted genes, Igf2r, Peg3 and Snrpn (P<0.05). Distinct IVM transcription patterns reflected the oocyte's response to its surrounding environment. Monitoring transcription levels of key oocyte maturation genes may subsequently assist in improving IVM success.