The collagen VI-related disorders (COL6-RDs) are a group of severe congenital neuromuscular disorders with no available treatment. New insight into its molecular characterisation together with the advance in the microscopy field offers the opportunity of making early diagnosis a quotidian process. In this study, three state-of-the-art microscopy techniques such as light sheet fluorescence microscopy (LSFM), second-harmonic generation (SHG) microscopy and fluorescence lifetime imaging microscopy (FLIM) are used to study a mouse model of the disorder. With these techniques parameters that define the pathological phenotype such as the cross-sectional area (CSA) of the muscle fibres, the distance between the myosin bands within the sarcomeres, and the differential lifetimes of the muscles autofluorescence can be compared to the wild type.