To gain insight into early embryo development, we used microarray technology to compare gene expression profiles in metaphase II oocytes and one- (1C), two- (2C) and four-cell (4C) embryos. Differences in spot intensities were normalised and grouped using Avadis Prophetic software platform (version 3.3; Strand Genomics, Bangalore, India) and categories were based on the PANTHER and Gene Ontology classification systems. We examined 6927 genes and identified those preferentially expressed in 1C or 2C embryos. We found 1261 genes that were more highly expressed (P < 0.05) in 1C compared with 2C embryos and 1480 genes showing enhanced expression in 2C embryos. Similarly, we investigated 6581 genes present in 2C and 4C embryos and identified 841 that are expressed to a greater extent at the 2C stage and 905 that are more highly expressed at the 4C stage. Using PANTHER classification, genes that were upregulated and downregulated in 2C embryos compared with 1C and 4C embryos were grouped according to their protein functions, which included developmental processes, electron transport, lipid, fatty acid and steroid metabolism, nucleoside, nucleotide and nucleic acid metabolism, protein metabolism and modification, signal transduction and transport, among others. Real time reverse transcription-polymerase chain reaction was performed to confirm differential expression of 14 selected genes. The identification of the genes being expressed will provide insight into the complex gene regulatory networks affecting zygotic genome activation and further development.