The Muscular Dystrophy Association (MDA) mission highlights a major goal of finding a cure for Duchenne Muscular Dystrophy (DMD). Currently, there is great excitement in the muscular dystrophy community as multiple ongoing gene-based therapies are advancing through clinical trials. These therapies utilize miniaturized dystrophin constructs, and these modified dystrophins are the focus of this study. We implemented a gene regulated system with high temporal and spatial specificity to determine the direct physiological significance of dystrophin protein deficiency including determining the half-life of truncated dystrophin in vivo. This system provides a robust means to investigate mechanistically how deletions in dystrophin affect therapeutically shortened dystrophin turnover in cardiac and skeletal muscle in vivo. We used a floxed allele approach together with a cardiac (αMHC) and skeletal (HSA) directed inducible Cre for precise control of dystrophin and micro-dystrophin gene excision. We examined the time course of full-length and micro-dystrophin mRNA as a biologically relevant surrogate for intact gene excision efficiency. Our data showed evidence of significant full-length dystrophin cDNA and micro-dystrophin gene excision, with a complete loss of micro-dystrophin mRNA and a gene excision efficiency of 80% for full-length dystrophin. Heart and skeletal tissues were extracted for protein quantitative analysis of micro-dystrophin (5, 10 and 30 days) and of full-length dystrophin (1, 3 and 6 months) post tamoxifen administration. Results demonstrate a fast turnover rate for micro-dystrophin in the heart and skeletal muscles, with calculated half-life of between 5-7 days in vivo. In marked contrast, full-length dystrophin was highly stable with dystrophin protein content (~ 40%) at 6 months, after dystrophin gene excision. Murf1 and Atrogin 1 were upregulated at the message level with Murf1 being also upregulated at the protein level in micro-dystrophin-derived skeletal muscle tissues compared to full length dystrophin, suggesting a possible involvement of Murf1 in the micro-dystrophin polyubiquitination and protein degradation pathway. Results from these studies will be highly informative in guiding the long-term success of ongoing and future DMD therapies featuring gene therapy with shortened dystrophins.