Little is known about the bovine intestinal microbiota influence on systemic innate immune responses. The objective of the present study was to determine relationships between acute-phase proteins in blood serum of cows [C-reactive protein (CRP), LPS-binding protein (LBP) and haptoglobin (Hp)] and the faecal microbiota. Fifty-two healthy cows (2–8 years old) were investigated. Faecal bacteria were determent characterized by in situ hybridization with 16S/23S rRNA-targeted probes and by conventional culture methods. The population of Gram-negative faecal bacteria (Enterobacteriaceae) was correlated negatively with CRP and positively with LBP in blood plasma, independent of the method used. Similar results were observed with Clostridium perfringens. No correlation was found between the faecal population of intestinal bacteria and Hp levels in blood plasma. This datum indicates that intestinal bacteria, especially Enterobacteriaceae and C. perfringens, may influence the level of CRP and LBP in blood plasma. These findings can be very important for diagnostic evaluations of the intestinal microbiota and provide specific information about its regulation.