Muscular dystrophies (MD) are a clinically and genetically heterogeneous group of Mendelian diseases. The underlying pathophysiology and phenotypic variability in each form are much more complex, suggesting the involvement of many other genes. Thus, here we studied the whole genome expression profile in muscles from three mice models for MD, at different time points: Dmd mdx (mutation in dystrophin gene), Large myd − / − (mutation in Large) and Dmd mdx /Large myd − / − (both mutations). The identification of altered biological functions can contribute to understand diseases and to find prognostic biomarkers and points for therapeutic intervention. We identified a substantial number of differentially expressed genes (DEGs) in each model, reflecting diseases' complexity. The main biological process affected in the three strains was immune system, accounting for the majority of enriched functional categories, followed by degeneration/regeneration and extracellular matrix remodeling processes. The most notable differences were in 21-day-old Dmd mdx , with a high proportion of DEGs related to its regenerative capacity. A higher number of positive embryonic myosin heavy chain (eMyHC) fibers confirmed this. The new Dmd mdx /Large myd − / − model did not show a highly different transcriptome from the parental lineages, with a profile closer to Large myd − / − , but not bearing the same regenerative potential as Dmd mdx . This is the first report about transcriptome profile of a mouse model for congenital MD and Dmd mdx /Large myd . By comparing the studied profiles, we conclude that alterations in biological functions due to the dystrophic process are very similar, and that the intense regeneration in Dmd mdx involves a large number of activated genes, not differentially expressed in the other two strains.