To determine if iron chelation therapy alters immune responses in children with cerebral malaria, we retrospectively measured mean serum levels of neopterin, interleukin-4 (IL-4), and IL-6 in children who received desferrioxamine B or placebo for three days in addition to quinine-based therapy. Mean levels of neopterin, IL-4, and IL-6 were elevated above the expected normal range on admission. Neopterin correlated significantly with the degree of anemia, IL-4 with the duration of fever prior to admission, and IL-6 with parasite density. Serial measurements of cytokines and neopterin were performed over four days in 39 children, 21 randomized to receive desferrioxamine B and 18 to receive placebo. Mean concentrations of neopterin did not change significantly in either group while levels of IL-4 increased significantly in the placebo group (P = 0.04) but remained unchanged in the desferrioxamine B group. Interleukin-6 concentrations decreased markedly in both groups (P < 0.025). Stable IL-4 levels in children given desferrioxamine B may represent an inhibition of the T helper lymphocyte-2 (TH-2) response resulting from a strengthened TH-1 response associated with iron chelation therapy. Any effect of iron chelation on immunity in the setting of severe malaria will have to be confirmed in future prospective investigations.