Immunological characteristics were assessed for prospective risk of clinical malaria in a longitudinally followed population in a holoendemic area of Tanzania. Baseline characteristics including crude Plasmodium falciparum extract-specific IgE and IgG; total IgE; and parasitological indices, e.g. number of P. falciparum clones, were investigated among 700 asymptomatic individuals. Cox regression analysis estimated the risk of succumbing to a new clinical episode during a 40 weeks follow up. High anti-P. falciparum IgE levels were associated with reduced risk of acute malaria in all age groups independently of total IgE levels. Statistically significant reduced odds ratio of 0.26 (95% CI, 0.09-0.72, P=0.010) and 0.44 (95% CI, 0.19-0.99, P=0.047) for the two highest fifths, respectively was observed after adjustment for age, sex, total IgE, numbers of parasite clones per infection and HIV-1 seropositivity. In contrast, high levels of malaria specific IgG or total IgE were not associated with reduced risk to succumb to a new clinical episode. A protective effect of asymptomatic multiclonal P. falciparum infections was also confirmed. For the first time, anti-malarial IgE levels in asymptomatic individuals in endemic area are found to be associated with reduced risk for subsequent malaria disease. Specific IgE antibodies may play role in maintaining anti-malarial immunity, or indicate other aspects of immune function relevant for protection against malaria.