A community-based baseline cross-sectional survey was conducted in three districts in Togo in September 2004 as part of a multidisciplinary evaluation of the impact of the Togo National Integrated Child Health Campaign. During this campaign, long-lasting-insecticide-treated bed nets (LLITNs) were distributed to households with children between 9 months and 5 years of age throughout the country in December 2004. The pre-intervention survey provided baseline malaria and anemia prevalence in children < 5 years of age during peak malaria transmission. Of 2,532 enrolled children from 1,740 households, 62.2% (1,352/2,172) were parasitemic and 84.4% (2,129/2,524) were anemic (hemoglobin < 11 g/dL). Moderate-to-severe anemia (< 8.0 g/dL) was found in 21.7% (543/2,524), with a peak prevalence in children 6-17 months of age and was strongly correlated with parasitemia (OR = 2.3, 95% CI: 1.8-2.5). Net ownership (mainly untreated) was 225/2,532 (8.9%). Subsequent nation-wide introduction of LLITNs and the introduction of artemisinin-based combination therapy have the potential to markedly reduce this burden of malaria.