Objectives This prospective study was designed to assess whether patients with skeletal deformities show characteristic masseter inhibitory reflex (MIR) and blink reflex (BR) patterns. A secondary aim was to investigate whether these reflexes change following bilateral sagittal split osteotomy (BSSO). Materials and methods Fourteen consecutive patients who underwent single-jaw BSSO and 14 class I subjects who constituted the control group were enrolled into the study. MIR and BR, obtained by the stimulation of supraorbital (SBR) and mental nerves (MBR), were electrophysiologically recorded. Sensory impairment in the mental nerve distribution was clinically tested. Three evaluation periods were specified as immediately before (T0), 1 month (T1) and 6 months (T2) after surgery. Results MIR early silent period duration was significantly shorter in the patients at T0 (p < 0.001). Sensory deficits developed on 23 sides after BSSO, of which, 17 recovered after 6 months. At T1, MBR was inelicitable bilaterally in 3 patients and unilaterally in 2 patients. These responses were still unrecordable bilaterally in 1 patient, and unilaterally in 4 patients at T2. MIR were unrecordable on 18 sides at T1 and recovered on 11 sides at T2. There were no parallels between the clinical sensory deficits and the abnormal results of the reflexes. Conclusions Shorter MIR in patients with dentofacial abnormalities may be a reflection of an adapted trigeminal reflex mechanism. Although MBR and MIR abnormalities do not develop parallel to the clinical sensory deficits, their course might provide insights into the disturbed trigeminal reflex pathways.