The objective of this study was to investigate the changes in synovial fluid concentration of collagen type II cleavage site (C2C) and procollagen II C-propeptide (CPII), markers of joint cartilage degeneration and synthesis, respectively, in horses with intraarticular fracture or osteochondrosis dissecans (OCD), and to examine the relationship between arthroscopic findings and these biomarker levels. Synovial fluid was collected from 36 joints in 18 horses (6 fractures and 12 OCDs). Samples from contralateral normal joints, when available, served as controls (n = 12). Concentrations of C2C and CPII were measured using enzyme-linked immunosorbant assays. Moreover, the severity of the cartilage degradation was graded arthroscopically in 16 horses, and the correlation between the C2C and CPII levels and the arthroscopic scores were investigated. Compared to the control, the concentration of C2C was increased in OCD joints but not in fracture joints, whereas the concentration of CPII was increased in fracture joints but not in OCD joints. Within each disease group there was no correlation between biomarker levels and arthroscopic findings. Therefore, although C2C and CPII have diagnostic potential further knowledge is required to provide accurate analysis.