SUMMARYA hypofunctional masticatory system was developed in 21-day-old male rats by feeding them a soft diet for 27 weeks. Retraining of a parallel group for 6 weeks was achieved by switching back to a hard diet after 21 weeks. A control group was fed a hard diet for 27 weeks. At the end of the experimental period, the expression levels of the myosin heavy chain isoform genes MYH 1 and 2 (fast), 3 (embryonic) and 7 (slow) in the deep masseter were compared using qRT-PCR analysis.The gene expressions of MYH 3 and MYH 7 were significantly higher in the rehabilitation group compared with the normal and hypofunctional group, but no significant differences were found in regards to the gene expression of MYH 1 and 2.Retraining made it possible for the slow (MYH 7) isoform levels to adapt to the increased mechanical load. The increased level of embryonic (MYH 3) isoform could be due to the need of creation of new MYH isoforms.