SummaryGene expression profiling ofin vivo- andin vitro-matured bovine oocytes can identify transcripts related to the developmental potential of oocytes. Nonetheless, the effects ofin vitroculturing oocytes are yet to be fully understood. We tested the effects ofin vitromaturation on the transcript profile of oocytes collected fromBos taurus indicuscows. We quantified the expression of 1488 genes inin vivo- andin vitro-matured oocytes. Of these, 51 genes were up-regulated, whereas 56 were down-regulated (≥2-fold) inin vivo-matured oocytes in comparison within vitro-matured oocytes. Quantitative real-time polymerase chain reaction (PCR) of nine genes confirmed the microarray results of differential expression betweenin vivo- andin vitro-matured oocytes (EZR, EPN1, PSEN2, FST, IGFBP3, RBBP4, STAT3, FDPSandIRS1). We interrogated the results for enrichment of Gene Ontology categories and overlap with protein–protein interactions. The results revealed that the genes altered byin vitromaturation are mostly related to the regulation of oocyte metabolism. Additionally, analysis of protein–protein interactions uncovered two regulatory networks affected by thein vitroculture system. We propose that the differentially expressed genes are candidates for biomarkers of oocyte competence.In vitrooocyte maturation can affect the abundance of specific transcripts and are likely to deplete the developmental competence.