We have previously demonstrated that rat cardiac troponin T (TnT) is expressed as two different isoforms during development, the larger, more acidic embryonic isoform and the smaller, more basic adult isoform, which appear to be generated from a common transcript of the cardiac TnT gene by alternative RNA splicing. In this study, Southern blot analysis confirmed the existence of a single copy of cardiac TnT gene in the rat genome. For investigation of the molecular mechanism of isoform switch and the control of this gene expression in myocardial development, several overlapping genomic clones were isolated from a rat genomic library. Complete nucleotide sequences were determined from these genomic clones and revealed a 19,186 base-pair DNA fragment containing 16 exons of rat cardiac TnT gene. Its DNA sequence and exon organization appeared to differ from that of the rat fast skeletal muscle TnT gene or chicken cardiac TnT gene. Comparison of genomic and cDNA clones also confirmed that the cardiac TnT isoform switching was due to the inclusion or exclusion of exon 4 during RNA processing. Sequence analysis allowed us to further identify the other alternatively spliced exon containing only nine nucleotides in size (exon 12). The inclusion and complete or partial exclusion of this exon may be responsible for generating three classes of mRNAs detected by our cDNA clones. The functional significance of this variation in TnT isoforms remained unknown, but its splicing pattern did not appear to link to the developmental changes. The 5' upstream structure was very similar to that in chicken cardiac TnT gene but differed from that in the rat fast skeletal muscle TnT gene, suggesting a similar regulatory mechanism for mammalian and avian cardiac TnT expression.