Knee pain and dysfunction has been often associated with an ineffective pull of the patella by the vastus medialis relative to the lateralis, particularly in individuals with knee joint malalignment. Such changes in muscular behaviour may be attributed to muscle inhibition and/or atrophy that precede the onset of symptoms. The aim of this study was to investigate possible effects of knee joint malalignment, indicated by a high Q-angle (HQ-angle >15° ), on the anatomical cross-sectional area (a-CSA) of the entire quadriceps and its individual parts, in a group of 17 young asymptomatic males compared to a group of 19 asymptomatic individuals with low Q-angle (LQ-angle <15° ). The a-CSA of the entire quadriceps (TQ), vastus medialis (VM), vastus lateralis (VL), vastus intermedius (VI), rectus femoris (RF) and patellar tendon (PT) were measured during static and dynamic magnetic resonance imaging (MRI) with the quadriceps relaxed and under contraction, respectively. A statistically significant lower a-CSA was obtained in the HQ-angle group, compared to the LQ-angle group for the TQ, VL and VI in both static (TQ=9.9%, VL=12.9% and VI=9.1%, P<0.05) and dynamic imaging (TQ=10.7%, P<0.001, VL=13.4%, P<0.01 and VI=9.8%, P<0.05) and the a-CSA of the VM in dynamic MRI (11.9%, P<0.01). The muscle atrophy obtained in the HQ-angle group may be the result of a protective mechanism that inhibits and progressively adapts muscle behavior, in order to reduce abnormal loading and wear of joint structures.