To determine the effects of n-3 PUFA supplementation on markers of inflammation in young horses in training, 16 Quarter Horses (2 to 4 yr) were used in a randomized complete block design for a 140-d trial. Treatments consisted of a control diet (n = 8) fed at 1% BW or a treatment diet (n = 8) of concentrate fed at 0.75% BW and 700 g of a marine n-3 supplement formulated to provide 15 g of eicosapentaenoic acid and 20 g of docosahexaenoic acid. Exercise protocol was divided into 2 phases: phase 1 (d 0 to 110) consisted of early training and phase 2 (d 111 to 140) consisted of advance maneuvers. Synovial fluid was obtained from the carpal joint every 28 d and analyzed for white blood cell count, total protein, and specific gravity. Blood samples were also collected at 28-d intervals for fatty acid analysis by gas chromatography, and concentrations of carboxypeptide type II collagen (CPII) and chondroitin sulfate-846 (CS-846) were determined by ELISA. Data were analyzed using the MIXED procedure of SAS. Plasma eicosapentaenoic acid and docosahexaenoic acid increased (P ≤ 0.01) in response to supplementation. However, diet did not affect serum CPII or CS-846 nor synovial white blood cell count, total protein, and specific gravity. Levels of CS-846 tended to increase over time (P = 0.09) and CPII concentration increased (P < 0.01) in response to changes in exercise. These results indicate further studies are needed to determine the efficacy of n-3 supplementation as a preventative measure against development of osteoarthritis.