BACKGROUND: Some studies have suggested that helminth infections increase the risk of malaria infection and are associated with increased number of malaria attacks and anaemia. Thus interventions to control helminth infections may have an impact on incidence of clinical malaria and anaemia. The current study assessed the impact of two anthelmintic treatment approaches on malaria infection and on anaemia in school and pre-school children in Magu district, Tanzania. METHODS: A total of 765 children were enrolled into a prospective randomized anthelmintic intervention trial following a baseline study of 1546 children. Enrolled children were randomized to receive either repeated treatment with praziquantel and albendazole four times a year (intervention group, 394 children) or single dose treatment with praziquantel and albendazole once a year (control group, 371 children). Follow up examinations were conducted at 12 and 24 months after baseline to assess the impact of the intervention. Stool and urine samples were collected and examined for schistosome and soil transmitted helminth infections. Blood samples were also collected and examined for malaria parasites and haemoglobin concentrations. Monitoring of clinical malaria attacks was performed at each school during the two years of the intervention. RESULTS: Out of 1546 children screened for P. falciparum, S. mansoni, S. haematobium, hookworm and T. Trichiura at baseline, 1079 (69.8%) were infected with at least one of the four parasites. There was no significant difference in malaria infection (prevalence, parasite density and frequency of malaria attacks) and in the prevalence of anaemia between the repeated and single dose anthelmintic treatment groups at 12 and 24 months follow up (p>0.05). However, overall, there was significant improvement in mean haemoglobin concentrations (p<0.001) from baseline levels of 122.0 g/L and 123.0 g/L to 136.0 g/L and 136.8 g/L for the repeated and single dose treatment groups, respectively, at 24 months follow-up which resulted in significant reduction in prevalence of anaemia. CONCLUSIONS: These results suggest that repeated anthelmintic treatment did not have an impact on malaria infection compared to single dose treatment. However, both treatment approaches had overall impact in terms of improvements of haemoglobin levels and hence reductions in prevalence of anaemia.