Proteoglycan fragments (PF) as chondroitin sulphate were monitored and compared in two groups of patients who had anterior cruciate ligament reconstruction with either patellar tendon (PT) or quadruple semitendinosus tendon (ST) autografts. There were 20 ST and 21 PT reconstructions. No difference existed between the groups in terms of associated lesion and time from injury to surgery. Synovial sample was collected at 6 weeks, 3 months and 18 months after the operation. No difference was noted between the groups at 18 months in terms of activity level and functional scores. Both groups demonstrated a sudden increase of PF at 6 weeks with respect to preoperative quantities (p<0.0001). A significant decrease occurred in the PT group at 3 months (p<0.008). Even at 18 months, it was significantly below the preoperative values (p<0.004). However, the decrease in ST cases relative to 6 weeks was insignificant at 3 months and quantities did not drop below the preoperative levels at 18 month (p=0.79). These results confirm again a gradual decrease of PF values in PT-reconstructed knees depending on time and surgery. Reconstruction with quadruple ST does not seem to have the same effect until 18 months postoperatively. Achievement of almost the same level of activity and function in both groups does not necessarily reflect the molecular status.