The purpose of this study was to monitor neuromuscular changes in quadriceps femoris muscle at 1 and 3 months after anterior cruciate ligament reconstruction (ACLR). Changes in isometric muscle strength (MVC), voluntary activation and surface electromyogram (EMG) parameters were examined in relation to knee stability, pain and swelling in 31 patients (25 M, 6 F) mean (SD) 30(8) years. Physically inactive (RC) and sports participants (SC) acted as controls. Median frequency (Hz) and amplitude (mV) of rectus femoris using Fast Fourier Transform (FFT) 2(11) was calculated during 5-s isometric contractions at 100, 75, 50 and 25% of MVC. One month after surgery, a significant correlation (P < 0.01) was found between activation (%) and MVC of injured knee extensors. By 3 months, most patients were pain free and had achieved full activation but still had muscle weakness. At 1 and 3 months post-surgery and for all levels of MVC contraction, the median frequencies of the injured limbs were significantly lower (P < 0.05) compared to the SC group as were those of the RC group. There was a significant lowering of the median frequencies of the uninjured limbs compared to the SC group at 75 and 100% of MVC. The EMG amplitude of the uninjured and injured limbs mirrored those of the SC and RC groups, respectively. These results support the view that muscle activation patterns were altered following ACL injury and surgical repair and may contribute to subsequent changes in muscle fibre properties during detraining and subsequent retraining.