The purpose of this study was to evaluate changes in biomarker and synovial parameters following autologous osteochondral transplantation (AOT) in the equine stifle joint, to test the hypothesis whether synovial parameters would show significant differences at selected time points following the surgery (at days 3, 14, 60 and 180) compared to baseline level (at day 0). Surgical intervention was performed in both stifles of nine horses (n = 18). The joints were randomly assigned to operated and sham-operated groups. Grafts 8.5 mm in diameter were harvested from the femoropatellar (FP) joint under arthroscopic control and the medial femorotibial (MFT) joints had AOT using mosaicplasty (MP) instrumentation, while the sham FP and sham MFT joints underwent arthroscopy and miniarthrotomy without transplantation, respectively. Synovial fluid (SF) parameters were evaluated at days 4, 14, 60 and 180. Data were analysed by two-way repeated-measures analysis of variance (ANOVA), and P < 0.05 was considered significant. During the first 10-14 days after surgery, lameness of degree 2-3/5 [American Association of Equine Practitioners (AAEP) scores] was present, which disappeared after 60 days. Joints with transplantation showed significant increases in synovial white blood cell count (WBC), total protein (TP), substance P, C1,2C and CS846 epitope concentration at day 3 compared to baseline and shamoperated joints (P < 0.05). These parameters returned to the baseline values by two months after surgery and remained within normal levels at 6 months postoperatively.