Central activation deficits have been recognised to be partially responsible for quadriceps muscle weakness after knee injuries effecting the injured as well as the uninjured leg. The purpose of this study was to assess the extent of bilateral activation deficits and its effect on functional muscle tests using the uninjured leg as reference. The study included 30 patients with isolated rupture of the anterior cruciate ligament (group 1), 42 patients with rupture of the anterior cruciate ligament and accompanying joint damage (group 2) and 34 healthy volunteers as reference. The maximum isometric knee extension torque and the maximal voluntary muscle activation (VA) were measured bilaterally using a sensitive twitch-interpolation method. The measured and the true functional deficit, adjusted to a physiological VA of the uninjured side, was calculated. Isolated rupture of the anterior cruciate ligament caused a minor VA-deficit and severe knee injuries more severe VA-deficits of the quadriceps muscles of the injured (VA group 1: 83.8 +/- 1.9 %; group 2: 76.9 +/- 1.8 %) and on the uninjured side (VA group 1: 85.9 +/- 1.8 %; group 2: 77.9 +/- 1.8 %) compared to the control group (VA 91 +/- 0.64 %). Due to contralateral VA-deficits the mean underestimation of the isometric muscle-force deficit was 22 % in group 1 and 48% in group 2. Unilateral knee injuries lead to significant VA-deficits of the quadriceps muscles on both the injured and uninjured legs related to the severity of injury. The validity of tests for the assessment of muscle function is questionable when using the uninjured side as reference.