During the pre-implantation period of embryonic development, the porcine embryo exhibits dramatic morphological changes associated with key developmental events such as cell cleavage, compaction and differentiation. Although these morphological landmarks can be identified during porcine pre-implantation development, the molecular mechanisms underlying these events are still not fully understood. To better elucidate these mechanisms at the level of gene expression, a comparative transcriptomic analysis of in vivo-derived porcine embryos representing 4 different early developmental stages (4-cell, morula, expanded blastocyst and hatched blastocyst) was performed with a custom designed porcine embryo-specific microarray from Agilent (http://embryogene.ca/). We identified 5,820, 5724, 7300 and 7639 annotated genes and 3473, 3229, 4812 and 4935 novel transcripts that are expressed in 4-cell, morula, expanded blastocyst, and hatched blastocyst stage porcine embryos respectively. In comparison with 4-cell stage embryos, 1,568 genes were commonly differentially expressed in morula, expanded blastocyst, and hatched blastocyst embryos. The results from PANTHER (Protein ANalysis THrough Evolutionary Relationships) analysis indicated that many of these differentially expressed genes are significantly enriched in developmentally-associated biological processes such as general metabolism, signal transduction, cell proliferation and apoptosis regulation. In addition, a significant enrichment in genes related to sex determination (including MAGOH, CLU, NSUN2 and ALG13) was also observed. The findings from this study will increase our understanding of the molecular mechanisms involved in early porcine embryonic development, and may help to identify candidate gene markers for viability and quality of early porcine embryos.