This review examines the mechanisms by which bioincompatibility in dialysis systems may have an effect on morbidity and mortality in the dialysis population. Direct toxic effects of membrane materials and various chemical substances have been well demonstrated in the chronic dialysis population. Activation of the complement cascade and stimulation of cytokine production may have autocrine effects on leukocyte function with sequelae such as enhanced rates of infection and the development of B2-microglobulin amyloidosis. The variable effect of different membrane materials on each of these effector systems is examined. Bioincompatibility may effect the incidence of infection, malignancy, cardiopulmonary disease, and malnutrition as well as induce novel disease processes. All these confounding variables must be considered when evaluating the effect of dialysis on mortality and morbidity.