This study aims to investigate the effect of in-feed clinoptilolite treatment on biomarkers such as serum amyloid A (SAA), haptoglobin, apolipoprotein A-I (APO A-I), and paraoxonase-1 (PON1) activity, triglycerides (TRIG) and high-density lipoprotein cholesterol in dairy cows with subclinical mastitis. A total of 69 Holstein dairy cows, aged 2-7 years, kept on a farm in North-Western Croatia, were included. Cows were randomly assigned into three groups: (1) Clinoptilolite (CPL) group with subclinical mastitis (n = 20), treated in-feed 50 g natural powdered clinoptilolite twice daily from 270th day of pregnancy to the end of study; (2) nontreated cows (n = 19) with subclinical mastitis (SCM); and (3) the control group (CON) of healthy cows (n = 30). Blood samples were taken: on the day of calving and on days 5, 12, 19, 26, 33, 40, and 60 after parturition. The concentration of SAA was highest in the SCM group (p < 0.001). PON1 activity was statistically significantly lower (p < 0.001) in cows from the SCM group than in the CPL and CON groups. Decreased PON1 activity and increased APO A-I were observed in the case of SCM. The positive effect of the addition of vibroactivated clinoptilolite in the feed of treated cows resulted in reduced values of APO A-I, SAA, and haptoglobin, and higher activity of PON1 during the two-month period of lactation after calving, on the basis of which we can assume that they may be less sensitive to infection in SCM.