The proteomics of inflammatory response in whey from cows with subclinical mastitis were analysed. Whey protein lysates were separated on 24 cm dry IPG strips (pH 3-10 linear) and 24 cm dry IPG strips (pH 4-7) using two-dimensional electrophoresis. The results indicated that the whey proteins in milk from cows with subclinical mastitis are different from those in milk from healthy cows. All protein spots were found to have biologically relevant changes in relative abundance during subclinical mastitis using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry analysis, including ß-1,4 galactosyltransferase, ß-2 microglobulin, complement 3, a-1-acid glycoprotein, ß-lactoglobulin A, a-S1 casein precursor, ß-casein B, and serotransferrin precursor. The mRNA expression of these genes was verified by quantitative real-time PCR. These proteins are involved in signal transduction, binding, transport, and immune defence activity. The results suggest that the markers may be used for the diagnosis of subclinical mastitis.