To reveal the effect of foreign innervation and altered thyroid status on fiber type composition and the myosin heavy chain (MyHC) isoform expression in the rat slow soleus (SOL) and fast extensor digitorum longus (EDL) muscles, a method of heterochronous isotransplantation was developed. In this experimental procedure, the SOL or EDL muscles of young inbred Lewis rats are grafted either into the host EDL or SOL muscles of adult rats of the same strain with normal or experimentally altered thyroid status. To estimate the extent of fiber type transitions in the transplanted muscles, the SOL and EDL muscle from the unoperated leg and unoperated muscles from the operated leg could be legitimately used as controls, but only when the experimental procedure itself does not affect these muscles. To verify this assumption, we have compared the fiber type composition and the MyHC isoform content of unoperated contralateral SOL and EDL muscles and ipsilateral unoperated SOL muscle of experimental rats after unilateral isotransplantation into the host EDL muscle with corresponding muscles of the naive rats of the same age and strain. We provide compelling evidence that the unilateral heterochronous isotransplantation has no significant effect on the fiber type composition and the MyHC isoform content of unoperated muscles of experimental animals. Hence, these muscles can be used as controls in our grafting experiments.