In this work, an alignment procedure of magneto-inertial units in the Special Orthogonal Space SO(3) is presented and discussed. The procedure, designed for ambulatory measurements of lower limb kinematic, is based on simple rotation movements around anatomical axes of hip joint and its accuracy is independent of the speed as well as the range of the movements. This is particularly important for movement analysis of subjects with motor impairments. Despite such procedure was designed for lower limb movement analysis, it can be applied to every anatomical compartment (e.g.: upper limb).