A treatment device and methods for HIFU treatment of thyroid and parathyroid disorders are provided. The treatment device comprises the first sensor for detecting swallowing motion and the second sensor for tracking the motion of the thyroid and parathyroid tissue with ultrasound imaging. Thus, the treatment device allows for safe and non-invasive use of HIFU on thyroid and parathyroid tissue of patients by synchronizing HIFU pulse delivery with patient swallowing and/or directing the applicator of HIFU energy to follow the appropriate tissue when the patient moves.