Anaemia remains an intractable public health problem in sub-Saharan Africa (SSA), owing largely to its complex and multifactorial causes. The absolute number of anaemia cases has increased by 50% in SSA from the year 1990 to 2010. To administer the appropriate treatment, identification of anaemia attributable to specific causes is required. In this paper, we assessed the relative contribution to anaemia of intestinal schistosomiasis (Schistosoma mansoni) and hookworm (a soil-transmitted helminth). The effect of S. mansoni on anaemia is controversial; this infection has not been found to consistently affect anaemia. However, hookworm has widely been shown to increase anaemia risk. Yet, limited information is available about the effect of S. mansoni and hookworm infections in populations that are not limited to children or pregnant women. Without this information, current World Health Organization guidelines for the treatment of anaemia due to intestinal helminths neglect a large portion of the general population by age and gender. To address this lack of information, we conducted a communitywide assessment of the effects of S. mansoni and hookworm infections on anaemia in rural Uganda.