The need for identification of specific modes of cell death, like apoptosis and necrosis, is driven by their detrimental or beneficial effect in different forms of disease, and the need in many instances of disease to modulate their levels. Apoptosis, an organized, gene-driven, and often energy-dependent mode of cell death, may be identified in tissue sections by its distinct morphological features, DNA degradation that is executed by endonucleases, and by presence of certain proteins, like the activated caspases. In the kidney, apoptosis is central to the development of a normal healthy kidney and it has been noted in glomeruli, the tubulo-interstitium, and renal vasculature in renal diseases or syndromes as diverse as acute kidney injury and chronic kidney disease of various causes, renal complications of diabetes and hypertension, sepsis, immune disorders and inflammation, nephrotoxicity, and in the development, progression, and treatment of renal cancers. Many research articles analyze apoptosis in tissue sections using the TUNEL assay that detects DNA strand breaks in situ in tissue sections. This method has been criticized because of false-positive or false-negative findings, and in situ analysis of activated caspase-3, thought to be the “executioner” caspase in the apoptotic pathway, may be a good alternative for quantifying apoptosis by light microscopy. The morphology of apoptosis, however, remains a standard that should not be ignored. This chapter reviews current methods of identifying apoptosis in tissue sections, with an emphasis on identification and quantification in the kidney using molecular methods.