Introduction To date, the proper choice of graft for anterior cruciate ligament (ACL) reconstruction remains a matter of conflict. We aimed to compare the clinical and functional outcomes of the two most commonly utilized autografts, bone-patella tendon-bone (BPTB) and four-strand hamstring tendon (HT) graft, at 6 and 12 months after surgery. Methods In a prospective randomized study, we included a total of 60 patients undergoing ACL reconstruction, thirty in BPTB and thirty in HT group. All patients were amateur athletes and were evaluated at 6 and12 months after surgery for: (a)postoperativefunctionality of the operated knee by the Tegner, the Lysholm and the International Knee Documentation Committee (IKDC) scoring scales, (b) anterior cruciate ligament (ACL) instability of the operated knee compared to the healthy contralateral knee by the KT-1000 arthrometer and (c) theextension and flexion muscle strength of the operated knee by a CYBEXisokinetic dynamometer. Results Patients in the two groups did not differ regarding demographics, and pre-injury functionality status. Significantly more patients in the HT group (n=6) compared to the BPTB group (n=1) experienced ACL re-rupture and underwent revision surgery before follow-up end (p=0.044). All patients, regardless of graft, showed significant improvement within each group of functional assessments by Lysholm, Tegner and IKDC scores, as well as of Cybex measurements -with an increase of peak torque at 60° extension and 180°extension and 60° flexion and 180° flexion- at 12 months compared to 6 months follow-up (p<0.05). However, there was no difference between the two groups regarding knee function improvement or extension measurements neither at 6 nor 12 months. Contrarily, the BPTB graft group had higher values of peak torque (Nm) at 60° and 180° flexion compared to the HT group, both at 6 (p=0.014 and 0.029, respectively) and 12 months (p=0.033 and 0.030, respectively). Postoperative stability was similar between the two groups at 12 months (p=0.519). Conclusion Both BPTB and HT grafts present with benefits and drawbacks and remain viable autograft options for primary ACL reconstruction as each has, although HT grafts seem to be more susceptible to re-rupture. The graft selection should be based on the needs and activities of each patient.