Cytokines play an important role in the regulation of normal immune function. In recent years cytokines and their receptors have been shown to be highly polymorphic. Polymorphisms in these genes have been associated with a number of immune diseases as well as organ transplant complications. The current disease association data is confusing and often contradictory. Whilst single locus analyses are the predominant form of cytokine polymorphism analysis, the use of polymorphic haplotypes is becoming increasingly common. This may help to give a clearer picture of the association of cytokine polymorphism with immune disfunction.