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Apheresis is the process of separating the blood and removing or manipulating a cellular or plasma component for therapeutic benefit. Such procedures may be indicated in the critical care setting as primary or adjunctive therapy for certain hematologic, neurologic, renal, and autoimmune/rheumatologic disorders. In part I of this series, the technical aspects of apheresis were described and the physiologic rationale and clinical considerations were discussed. This review highlights the pathophysiologic basis, specific clinical indications, and treatment parameters for disorders that more commonly require management in the intensive care unit. The choice of plasma or cellular apheresis in these cases is guided by well-accepted evidence-based clinical treatment guidelines. For some disorders, such as liver failure, severe sepsis, and multiple-organ dysfunction syndrome, apheresis treatment approaches remain experimental. Ongoing studies are investigating the potential utility of conventional plasma exchange, ex vivo plasma manipulation, and newer technologies for these and other disorders in severely ill patients.