The expression and regulation of endometrial proteins are crucial for conceptus implantation and development. However, little is known about site-specific proteome profiles of the mammalian endometrium during the peri-implantation period. We utilized two-dimensional gel electrophoresis/mass spectrometry-based proteomics approach to compare and identify differentially expressed proteins in sheep endometrium. Caruncular and intercaruncular endometrium were collected on days 12 and 16 of the oestrous cycle and at three stages of pregnancy corresponding to conceptus pre-attachment (day 12), implantation (day 16) and post-implantation (day 20). Abundance and localisation changes in differentially expressed proteins were determined by Western blot and immunohistochemistry. In caruncular endometrium, 45 protein spots (5% of total spots) altered between days 12 and 16 of pregnancy while 85 protein spots (10% of total spots) were differentially expressed between day 16 of pregnancy and day 16 of the oestrous cycle. In intercaruncular endometrium, 31 protein spots (2% of total spots) were different between days 12 and 16 of pregnancy while 44 protein spots (4% of total spots) showed differential expression between days 12 and 16 of the oestrous cycle. The pattern of protein changes between caruncle and intercaruncle sites were markedly different. Among the protein spots with implantation related changes in volume, 11 proteins in the caruncular endometrium and 6 proteins in the intercaruncular endometrium, with different functions such as protein synthesis and degradation, antioxidant defence, cell structural integrity, adhesion and signal transduction, were identified. Our findings highlight the different but important roles of the caruncular and intercaruncular proteins during early pregnancy.