Pregnancy is a physiological state that can be described, from a biochemical point of view, using protein patterns. The present study focused on the comparison of protein patterns between the saliva and plasma of pregnant cows to search for possible markers which are present both in plasma and saliva. Saliva and plasma were collected from healthy, pregnant (3–4 months) and non-pregnant (C; n = 4) cows aged between 4 and 8 years (P; n = 8) from the same farm. Biological material was analyzed using 2D electrophoresis and MS identification. Among identified spots, there were those which could be related to pregnancy (e.g., apolipoproteins I and II in all examined matrices or transforming growth factor-beta-induced protein ig-h3 in albumin-free plasma) as well as those which are responsible for regulating of cellular processes (e.g., pyruvate kinase and aspartate aminotransferase in all examined matrices, or lactate dehydrogenase, phosphoglycerate kinase, and NADH dehydrogenase in plasma). Further identification of common spots and those only specific to saliva as well as the comparison between other periods of pregnancy are necessary; it is already clear that saliva can be considered a valuable diagnostic matrix containing potential markers of physiological and pathological status.