This mini-review summarizes the results of recent transcriptome studies of bovine endometrium during the estrous cycle and during the pre-implantation phase, with a focus on immune response genes. Gene expression changes in the bovine endometrium during the estrous cycle were compared to a similar study in equine endometrium. The results indicate species-specific expression patterns, particularly for genes with immune functions. These are presumably the consequence of adaptations to differences in the physiology of reproduction in each species, including development of the conceptus, hormone profiles during the estrous cycle, and insemination. The results from a number of transcriptome studies during the pre-implantation phase, as well as comparison to the effects of human interferon alpha on bovine endometrial gene expression, suggest that during pregnancy there is no general suppression of the maternal immune system, but rather a fine-tuned regulation of immune cells. This presumably facilitates tolerance to the immunologically 'foreign' conceptus and at the same time activation of the immune system to defend against microbial and viral infections. Furthermore, comparison of differentially expressed genes in bovine endometrium to similar studies in human endometrial samples reveals a number of similar changes, indicating the existence of shared mechanisms in preparation for embryo implantation., (Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.)