An alternative RNA splicing-generated cardiac troponin T (cTnT) isoform switching has been found during both avian and mammalian heart development. The present study demonstrates that the mouse cTnT isoform switching is approximately 10 days earlier than that in rat during perinatal heart development. The mouse cTnT isoform switching is also approximately 10 days earlier than the transcriptionally regulated troponin I (TnI) isoform switching, a transition that showed similar timing during mouse and rat heart development. In addition, synchronized cTnT and TnI switches are observed during both rat and chicken heart development. More interestingly, the expression of cTnT in both mouse and rat neonatal skeletal muscles showed an isoform transition pattern synchronized with the cTnT isoform switching in the neonatal heart of the corresponding species. The results suggest that the alternative RNA splicing-generated cTnT isoform switching during development is (a) not a direct response to the functional changes in perinatal myocardium and (b) not a restricted regulation in the heart, but is controlled by a species-specific programming that is synchronized in developing cardiac and skeletal muscles.