This study investigates gender differences in lateral trunk lean to confound possible associations with hip and knee joint biomechanics during lateral reactive jumps. Twelve female and 12 male athletes performed lateral reactive jumps while three-dimensional knee, hip and trunk kinematics as well as ground reaction forces and electromyography of selected thigh muscles were recorded. Lateral trunk lean did not differ between genders, while females had greater knee valgus angle than males (-4.9 ± 3.9° vs. 1.6 ± 3.2°, p = 0.001). A significant association between the lateral trunk lean and the hip abduction moment (r = 0.55) was found. Moreover, lateral trunk lean and knee abduction moment showed a significant relationship (r = 0.67). The positive association between trunk lean and knee abduction moment suggests that higher lateral trunk lean may increase the risk of knee injury during lateral movements and that the trunk should be trained accordingly in team sports.