Fish oil supplementation has been reported to be generally beneficial in autoimmune, inflammatory and cardiovascular disorders. Most researchers have attributed these beneficial effects to the high content of omega-3 fatty acids in fish oil (FO). The effects of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are not differentiated in most studies. In fact, up to 1990, purified DHA was not available for human use and there was no study regarding its effects on human immune response. In this review, the differences in the effects of these two fatty acids on cell function are discussed. Studies have shown that EPA and DHA have also different effects on leukocyte functions such as phagocytosis, chemotactic response and cytokine production. DHA and EPA modulate differently expression of genes in lymphocytes. Activation of intracellular signaling pathways involved with lymphocyte proliferation is also differently affected by these two fatty acids. In relation to insulin producing cell line RINm5F, DHA and EPA are cytotoxic at different concentrations and the proteins involved with cell death are differently modulated by these two fatty acids. Substantial improvement in the therapeutic usage of omega-3 fatty acid-rich FO will be possible with the discovery of the different mechanisms of actions of DHA and EPA.