3D joint kinematics can provide important information about the quality of movements. Optical motion capture systems (OMC) are considered the gold standard in motion analysis. However, in recent years, inertial measurement units (IMU) have become a promising alternative. The aim of this study was to validate IMU-based 3D joint kinematics of the lower extremities during different movements. Twenty-eight healthy subjects participated in this study. They performed bilateral squats (SQ), single-leg squats (SLS) and countermovement jumps (CMJ). The IMU kinematics was calculated using a recently-described sensor-fusion algorithm. A marker based OMC system served as a reference. Only the technical error based on algorithm performance was considered, incorporating OMC data for the calibration, initialization, and a biomechanical model. To evaluate the validity of IMU-based 3D joint kinematics, root mean squared error (RMSE), range of motion error (ROME), Bland-Altman (BA) analysis as well as the coefficient of multiple correlation (CMC) were calculated. The evaluation was twofold. First, the IMU data was compared to OMC data based on marker clusters; and, second based on skin markers attached to anatomical landmarks. The first evaluation revealed means for RMSE and ROME for all joints and tasks below 3°. The more dynamic task, CMJ, revealed error measures approximately 1° higher than the remaining tasks. Mean CMC values ranged from 0.77 to 1 over all joint angles and all tasks. The second evaluation showed an increase in the RMSE of 2.28°- 2.58° on average for all joints and tasks. Hip flexion revealed the highest average RMSE in all tasks (4.87°- 8.27°). The present study revealed a valid IMU-based approach for the measurement of 3D joint kinematics in functional movements of varying demands. The high validity of the results encourages further development and the extension of the present approach into clinical settings.