The cell dying by apoptosis undergoes a sequence of morphological, biochemical, and molecular changes which are characteristic, and often unique, to this mode of cell death. Specific features of apoptotic cells resulting from these changes, which serve as markers used to reveal the apoptotic mode of cell death and to quantify the extent of apoptosis in cultures or in tissue, are reviewed. Analysis of these features by flow or image cytometry is the most commonly used approach to detect, quantify, and study various aspects of apoptosis. Flow or laser scanning cytometry also offer all the advantages of rapid, accurate and multiparametric measurements to investigate the biological processes associated with cell death. Numerous methods have been developed to identify apoptotic and necrotic cells, which are widely used in various disciplines, particularly in oncology and immunology. The methods based on changes in cell morphology, plasma membrane molecular structure and transport function, function of cell organelles, DNA stability to denaturation and endonucleolytic DNA degradation are reviewed and their applicability in the research laboratory and in the clinical setting is discussed. The most common pitfalls and improper use of the methodology in analysis of cell death and in data interpretation are also discussed.