Introduction: A microarray study showed an increase of developmental myosin heavy chain (MyHC) mRNA in the masseter muscle after surgery. The aim of the study was to determine the expression of the embryonic MYH3 and perinatal MYH8 for use as potential marker for muscle adaptation after orthognathic surgery. Material and methods: 24 adult patients with a prognathic (11) or retrognathic (13) mandible were involved in the study. 192 biopsies were taken from two parts of the muscles presurgically and 6 months following. The expression of MYH3 and MYH8 were quantified using real-time polymerase chain reaction (RT-PCR). Absolute quantification was done by CT-values. Results: MYH3 was up-regulated in prognathia (8.5, P < 0.001) and in retrognathia (2.8, P < 0.043). MYH8 was up-regulated in retrognathia only (4.0, P < 0.063) and down-regulated in prognathia (-1.6). MYH3 values correlated in retrognathic patients (P < 0.005) before and after surgery. Conclusion: MYH3 and MYH8 could play a role in functional adaptation after orthognathic surgery and orofacial orthopaedics.