Magnetic inertial measurement unit systems (MIMU) offer the potential to perform joint kinematics evaluation as an alternative to optoelectronic systems (OS). Several studies have reported the effect of indoor magnetic field disturbances on the MIMU's heading output, even though the overall effect on the evaluation of lower limb joint kinematics is not yet fully explored. The aim of the study is to assess the influence of indoor magnetic field distortion on gait analysis trials conducted with a commercial MIMU system. A healthy adult performed gait analysis sessions both indoors and outdoors. Data collected indoors were post-processed with and without a heading correction methodology performed with OS at the start of the gait trial. The performance of the MIMU system is characterized in terms of indices, based on the mean value of lower limb joint angles and the associated ROM, quantifying the system repeatability. We find that the effects of magnetic field distortion, such as the one we experienced in our lab, were limited to the transverse plane of each joint and to the frontal plane of the ankle. Sagittal plane values, instead, showed sufficient repeatability moving from outdoors to indoors. Our findings provide indications to clinicians on MIMU performance in the measurement of lower limb kinematics.