Tissue clearing techniques turn tissue transparent through a series of chemical and physical treatments. They have provided a useful tool for three-dimensional (3-D) imaging to study tissue spatial organization and interactions. Many tissue clearing methods have been developed in recent years. Each method has its own application range depending on the purposes of the study. Three criteria for selecting an appropriate clearing method include clearing transparency, fluorescence preservation, and broad tissue applicability. PEG-associated solvent system (PEGASOS) emerged recently as a solvent-based tissue clearing method capable of rendering diverse tissues highly transparent while preserving fluorescence. Combined with vascular labeling techniques, PEGASOS method enables 3-D visualization of vasculature in whole tissues at subcellular resolution. Here, we describe the standard PEGASOS passive immersion protocol and several compatible vascular labeling techniques. Methods of 3-D imaging, data processing, and annotations are also briefly introduced.