The collection and processing of frozen muscle tissue is essential for accurate downstream analysis of human and animal samples collected in Duchenne muscular dystrophy (DMD) research. Specific techniques are essential for preserving the tissue morphology and molecular markers that are vital for diagnostics, evaluation of disease progression, and preclinical in vivo research. Freezing muscle tissue in liquid nitrogen-cooled isopentane maintains tissue structure and preserves enzyme activity, which is crucial for enzyme histochemistry and other downstream protein analysis. In this chapter, we will discuss techniques for tissue handling, cryo-sectioning, and staining to minimize preparatory artifacts ensure optimal performance of downstream assays.