Hamstring muscle group dysfunction following anterior cruciate ligament reconstruction (ACL) using a semitendinosus-gracilis autograft is a growing concern. This study compared the mean peak isometric knee flexor torque of the following three groups: subjects 2 years following ACL reconstruction using semitendinosus-gracilis autografts (Group 1), subjects 2 years following ACL reconstruction using tibialis anterior allografts (Group 2), and a non-injured, activity-level-matched control group (Group 3). We hypothesized that Group 1 would have greater mean involved lower extremity peak isometric knee flexor torque deficits than the other groups. Handheld dynamometry with subjects in prone and the test knee at 90 degrees flexion was used to determine bilateral peak isometric knee flexor torque. Group 1 (86.4 +/- 11) and Group 2 (80.5 +/- 13) had similar 2000 IKDC Subjective Knee Evaluation Form scores (P = NS). Group 1 had a mean involved lower extremity peak isometric knee flexor torque deficit of -17.0 +/- 14 Nm. Group 2 had a mean involved lower extremity peak isometric knee flexor torque deficit of -0.8 +/- 9 Nm. Group 3 (control) had a mean left and right lower extremity peak isometric knee flexor torque difference of -0.7 +/- 14 Nm. Group 1 had decreased involved lower extremity peak isometric knee flexor torque compared to Groups 2 and 3 (two-way ANOVA; group x side interaction P < 0.05, Tukey HSD = 0.008). Long-term knee flexor strength deficits exist following hamstring autograft use for ACL reconstruction that does not occur when a tibialis anterior allograft is used. Early identification of impaired knee flexor strength among this group and modified rehabilitation may reduce these deficits. Adding quantitative biomechanical testing of sprinting and sudden directional change movements to the standard physical therapy evaluation will better elucidate the clinical and functional significance of the observed knee flexor strength impairments and aid in determining sport specific activity training readiness.