Studies performed in Burkina Faso and Mali showed differences in susceptibility to malaria between the Fulani and other sympatric ethnic groups, the Mossi and Dogon. We carried out a longitudinal survey and three cross-sectional studies from 2003 to 2005 in order to assess the prevalence of anemia in Dogon and Fulani. The distribution of the study population by sex was comparable between the two ethnic groups (p = ns). The Fulani are mainly cattle breeders and the Dogons, farmers. They were exposed to similar entomological inoculation rates, and studies on "knowledge, attitude, and practices" showed no difference between the two ethnic groups. The cross-sectional studies were performed during the intense malaria transmission season (in September 2003 and 2005) and during the dry season (in March 2004). Longitudinal clinical follow-up studies were performed from August to December 2005 using the WHO 28 days in vivo test, after administration of a curative dose of antimalarial drugs to patients with mild malaria. During the cross-sectional studies, both Fulani men and women had significantly lower hemoglobin levels than their Dogon counterparts; this difference was most evident in the women (in 2005: 9.4 g/dl in Fulani vs 10.7 g/dl in Dogon, p = 0.0002). Clinical longitudinal follow-up data showed that Fulani children aged 10-14 years have lower hemoglobin levels than Dogon children. At day 0, the mean of hemoglobin level was 9.6 g/dl in Dogon children vs. 8.7 g/dl in Fulani children (p = 0.01). At day 28, after malaria treatment, we also observed a significant difference in hemoglobin levels in children (10.6 g/dl in Dogon vs 9.3 g/dl in Fulani, p < 0.001). A stronger association between anemia and spleen enlargement was found in the Fulani (53.2% with spleen enlargement) than in the Dogon (32.9%) [p = 0.005]. The Fulani suffer more from anemia than the Dogon, despite their lower susceptibility to malaria. The difference in anemia between Dogon and Fulani must be further investigated to determine possible factors involved in malaria susceptibility.