Veterinarians can recommend milk thistle for the treatment of equine liver disease and laminitis. Milk thistle seed cakes were fed in the range of normal feed doses in this study. The milk thistle seed cakes were fed (twice a day) to the experimental group of the horses (n = 5) and biochemical blood markers (TP, Albumin, ALT (alanine transaminase), AST (aspartate transaminase), ALP (alkaline phosphatase), GGT (gamma-glutamyltransferase), Bilirubin, Cholesterol, HDL (high-density lipoprotein), LDL (low-density lipoprotein), TAG (triacylglycerol), BHB (beta-hydroxybutyric acid), NEFA (non-esterified fatty acids), creatine kinase, creatinine, Urea, GSH-Px (glutathione peroxidase), TAS (total antioxidant status), lactate, glucose, cortisol, Ca, Pi) were monitored. The control group of horses (n = 5), bred and trained in the same conditions, was used for comparison. The control group received the entire feed dose as accepted by the horses in the experimental group before the beginning of the experiment. The aim was to find out whether the preparation of milk thistle seed cakes could have positive effects on the health of the horses. All ten horses received one feeding form before the beginning of the experimental monitoring. All horses were exposed to heavy physical exercise (regular combined driving training) after 56 days of milk thistle seed cakes feeding (up to 400 g/day). Three blood samples were taken (before physical exercise; about 15 min and 60 min after physical exercise). Significant differences (p < 0.05) were detected in the values of AST, NEFA, cortisol and Pi in the experimental group. The exercise effect was detected in the values of albumin, lactate, cortisol, NEFA, and calcium. Our results suggest that the feeding of milk thistle seed cakes could have a positive effect on the health of the horses.