Polypyrimidine Tract Binding Protein (PTB) regulates pre-mRNA splicing, having special relevance for determining gene expression in the differentiating muscle. We have previously shown that PTB protein abundance is progressively reduced during heart development without reduction of its own transcript. Simultaneous reduction of Histone Deacetylase (HDAC) expression prompted us to investigate the potential link between these events. HDAC5-deficient mice have reduced cardiac PTB protein abundance, and HDAC inhibition in myocytes causes a reduction in endogenous expression of cFLIP and caspase-dependent cleavage of PTB. In agreement with this, cardiac PTB expression is abnormally high in mice with cardiac-specific executioner caspase deficiency and cellular FLICE-like inhibitory protein (cFLIP) overexpression prevents PTB cleavage in vitro. Caspase-dependent cleavage triggers further fragmentation of PTB and these fragments accumulate in the presence of proteasome inhibitors. Experimental modification of the above processes in vivo and in vitro results in coherent changes in the alternative splicing of tropomyosin-1 (TPM1) and tropomyosin-2 (TPM2) and Myocyte Enhancer Factor-2 (Mef2) genes. Thus, we report a pathway connecting HDAC, cFLIP and caspases regulating the progressive disappearance of PTB, which enables the expression of the adult variants of proteins involved in regulation of contraction and transcription during cardiac muscle development.