Cardiac myosin heavy chain (MHC) gene expression undergoes a rapid transition from to MHC during early rodent neonatal development (0 to 21 days of age). Thyroid hormone (T3) is a major player in this developmental shift; however, the exact mechanism underlying this transition is poorly understood. The goal of this study was to conduct a more thorough analysis of transcriptional activity of the cardiac MHC gene locus during the early postnatal period in the rodent, in order to gain further insight on the regulation of cardiac MHC genes. We analyzed the expression of the two cardiac MHC isoforms ( and MHC) at the protein, mRNA and pre-mRNA level at birth and at 7, 10, 15 and 21 days after birth in both euthyroid and hypothyroid rodents. Using novel technology, we also analyzed RNA expression across the cardiac gene locus and we uncovered that the intergenic (IG) region between the two cardiac genes possess bidirectional transcriptional activity. This intergenic transcription results in an antisense RNA product as described previously, which is thought to exert an inhibitory effect on the MHC gene transcription. On the second half of the IG region, sense transcription occurs resulting in expression of a sense IG RNA that merges with the MHC pre-mRNA. This sense IG RNA transcription was detected in the MHC gene promoter, ~-1.8kb relative to the MHC TSS. Both sense and antisense IG RNAs were developmentally regulated and responsive to a hypothyroid state. This novel observation provides more complexity to the cooperative regulation of the two genes suggesting the involvement of epigenetic processes in the regulation of cardiac MHC gene locus.