To investigate the association between serum biomarker [cartilage oligomeric matrix protein (COMP) and matrix metalloproteinase-3 (MMP-3)] levels and clinical, magnetic resonance imaging (MRI), and arthroscopic findings in anterior cruciate ligament (ACL)-deficient knees without osteoarthritic changes on radiographs. Patients with ACL injury of Kellgren-Lawrence grade 0 or 1 were enrolled. Serum COMP and MMP-3 levels were measured preoperatively. Correlations of serum biomarker levels with age, body mass index (BMI), duration from time of injury, Tegner activity scale (TAS) score, Lysholm knee score, International Knee Documentation Committee score, KT-1000 arthrometer measurements, whole-organ MRI score (WORMS), MRI T2 relaxation time, and arthroscopic International Cartilage Research Society (ICRS) grade were assessed by calculating Spearman correlation coefficients. Associations between intraoperative findings (cartilage, meniscus) and serum biomarker levels were determined using the Mann-Whitney U test. Multiple regression analysis was performed to investigate the correlations between serum biomarker levels and MRI and arthroscopic findings. Ninety-eight patients with a mean age of 23.7 years were enrolled. Higher serum COMP level was correlated with older age and higher BMI, TAS score, serum MMP-3 level, WORMS, and T2 relaxation times (medial femur, medial tibia). Multivariate analysis showed that the serum COMP level was independently associated with WORMS and ICRS grade. The serum COMP level was correlated with age, BMI, TAS score, and MMP-3 level in ACL-deficient knees and was independently correlated with WORMS and ICRS grade. Thus, the serum COMP level can help detect cartilage degeneration even in patients without radiographic osteoarthritic changes. Key Points • Serum COMP correlated with WORMS and ICRS grade in ACL deficient knee. • The serum COMP level could help in detecting cartilage degeneration, even in patients with no radiographic osteoarthritic changes.