Immunostaining enables the detection of proteins and antigens in histological preparations due to specific antigen–antibody interactions. Such visualization can be performed by immunoperoxidase methods, but more recently, we have switched to immunofluorescence methods that offer superior sensitivity and simultaneous detection of multiple antigens. Key to this approach is a counterstaining method that masks tissue histofluorescence and the autofluorescent storage material that accumulates in the disorders we study. Such methods allow the analysis of the structural organization of lysosomes and the impact of their dysfunction on cells and tissues. In this chapter, we present an optimized staining protocol that can serve as a standard procedure in histological examinations, ensuring high quality and consistency of quantitative results.