Patellar tendon shortening after anterior cruciate ligament reconstruction may be associated with anterior knee pain or patellofemoral arthritis. The present study was designed to compare postoperative changes in patellar tendon length after anterior cruciate ligament reconstruction between patellar tendon and hamstring tendon autograft. Magnetic resonance images of both knees (operated and healthy) and functional outcome were documented at least 1 year postoperatively in 16 patellar tendon harvested patients and in 32 hamstrings harvested patients. Patellar tendon length, patella length and Insall-Salvati ratio were measured. The operated knee values were compared to the respective values of the non-operated control knees. A significant 4.2 mm or 9.7% patellar tendon shortening in patellar tendon group and a non-significant 1.14 mm or 2.6% shortening in hamstrings group was detected. No significant difference was detected in terms of major shortening-patella baja-(6% for the patellar tendon group vs. 0% for the hamstring group). There was no significant difference in anterior knee problems between the two groups as evidenced by the Shelbourne score (94 for the patellar tendon group vs. 98 for the hamstring group). Harvesting of the patellar tendon for anterior cruciate ligament reconstruction resulted in a significant shortening of the remaining tendon. In contrast harvesting of the hamstring tendons did not affect significantly the patellar tendon length. However, the incidence of patella baja and overall functional outcome was not significantly different between the two groups.