Cells undergo apoptosis during development, tissue homeostasis, and disease, and are rapidly cleared by both professional and nonprofessional phagocytes. In the whole animal, this process is remarkably efficient and usually goes unnoticed. It is estimated that 2 � 1011 cells are cleared each day and it has been suggested that detection of apoptotic cells in tissues should lead one to at least question the presence of a local clearance defect. For the last two decades, in vitro phagocytosis assays have played a critical role in identifying the receptors and mechanisms involved in the recognition and ingestion of apoptotic cells. The methodology of phagocytosis assays can be broken down into four separate components: apoptosis induction in target cells, preparation of phagocytes, the interaction assay, and the quantitative assessment of apoptotic cell engulfment. Here, we attempt to provide a detailed description of all the individual components of this complex procedure. To date, this has not been done in its entirety but is vital for the accurate assessment of stimuli that influence the clearance process.