Due to the small size of the mouse, evaluating its clinical phenotype is sometimes problematic. In contrast, mouse models are readily accessible to post-mortem analyses at any time during the course of a disease and prior to its clinical onset. RNA, protein, and histological analyses following sacrifice represent a powerful means to identify affected cell types and molecular events underlying the altered phenotype, and therefore to understanding the signaling or metabolic pathways involved. In this unit, an overview of post-mortem analyses is provided with a strong emphasis on the principles of routine histology, including tissue fixation, processing, embedding, and staining with hematoxylin and eosin. There are also several protocols for staining with specialized histological stains used in the metabolic field to detect intracellular lipids, intracellular lipid “ghosts”, cholesterol esters, polysaccharides, mitochondria, pathological collagen deposits, and atherosclerotic plaques