Aims: Myostatin (Mstn) is a member of the transforming growth factor-β (TGF-β) family that inhibits muscle differentiation. In this study, we aimed to identify the relationships between Mstn, thyroid hormone receptor alpha (TRα), and myosin heavy chain (MyHC) isoform expression during early postnatal development. Methods: We investigated the expression of Mstn, TRα, and MyHCs (embryonic, slow, IIa, IIb, and IIx) using quantitative real-time RT-PCR and ELISA (Mstn) in postnatal mouse muscles between day 0 and day 10. We also examined the correlations between Mstn, TR and MyHCs during the early development of mouse masseter muscle (MM) and rectus femoris muscle (RFM). Results: Distinct Mstn mRNA expression patterns were observed in the two muscles despite nearly non-significant changes in the Mstn protein abundance in MM. The expression pattern of the TRα mRNA in the MM differed from that observed in the RFM. The expression of MyHC IIa, IIb and IIx mRNAs increased in the MM and decreased in the RFM from day 0 to day 10, whereas embryonic fiber MyHC mRNA expression was similar in both muscle types. Principal component analysis showed the existence of a correlation between: (1) TRα and MyHC, (2) Mstn and MyHC, and (3) TRα and Mstn in MM. The correlations were different in RFM and MM. Cluster analyses identified the distinct clusters: cluster 1, days 0-4 for the MM and day 0 for the RFM;cluster 2, day 6 for the MM and day 2 for the RFM; and cluster 3, days 8-10 for the MM and days 4-10 for the RFM. Conclusions: These data suggest that TRα influences MyHC expression in both muscle types. In addition, Mstn has a limited effect in the MM related to the expression of individual MyHCs, as opposed to its role in the RFM, at early postnatal developmental stages. TRα could be involved in regulating both the temporal expression of MyHCs and Mstn at the early postnatal stages in the MM and RFM.