. A comparison was made of the prevalence of malaria and helminth coinfection among schoolchildren in Tanzania. Children in rice irrigated ecosystems were at highest risk of acquiring coinfections than those from sugarcane or savannah ecosystems. Display omitted ► Sixty percent of children in Tanzania have at least an infection of either Plasmodium falciparum or helminth. ► Co-infections of P. falciparum+W. bancrofti and P. falciparum+S. haematobium are most prevalent. ► Children from rice irrigated ecosystems are at highest risk of acquiring double, triple or quadruple infections. ► Malaria-helminth co-infections are prevalent among children and the pattern varies between agro-ecosystems. In Sub-Saharan Africa, some individuals infected with malaria are also infected with helminths. However, the magnitude and distribution of such coinfections in relation to eco-systems remains poorly defined. This study was undertaken to determine the prevalence of Plasmodium falciparum and helminth coinfections among schoolchildren in relation to agro-ecosystems in Mvomero District, Tanzania. The agro-ecosystems were categorised as sugarcane, traditional flooding rice irrigation, improved non-flooding rice irrigation and savannah. Schoolchildren had their blood examined for P. falciparum and Wuchereria bancrofti; urine for Schistosoma haematobium and stool for intestinal helminths. Blood samples were also examined for haemoglobin concentration. A total of 578 schoolchildren (mean age=7.96 years) were involved in the study. Overall, 60% of all schoolchildren had at least an infection of either P. falciparum, W. bancrofti, S. haematobium or hookworm. The highest prevalence of P. falciparum (75.3%), W. bancrofti (62.9%) and hookworm (24.7%) infections was observed among children in flooding rice irrigation ecosystem. P. falciparum+S. haematobium (10.9%) and P. falciparum+W. bancrofti (11.1%) were the most prevalent types of coinfection in the area. The highest prevalence of double parasitic infections was observed among children in the flooding rice irrigation ecosystems. The risk for acquiring coinfections of P. falciparum+W. bancrofti was significantly higher among children in the flooding rice irrigation ecosystem. Forty-five (7.8%) children were coinfected with three types of parasitic infections. The risk of acquiring triple infection among children from flooding rice irrigation was higher for P. falciparum+S. haematobium+W. bancrofti (p<0.001). Seven schoolchildren (1.2%) were found infected with four parasites and all were from the flooding rice irrigation ecosystem. Significantly high P. falciparum geometric parasite density was observed among children coinfected with either hookworms or W. bancrofti (p<0.001). On average, 17.8% (103/578) of the children had enlarged spleens. Over 3- and 4-folds increase in the risk of having an enlarged spleen were observed among children coinfected with P. falciparum+S. haematobium and P. falciparum+W. bancrofti, respectively. The overall prevalence of anaemia (<11.5g/dl) was 61.9% (358/578). Malaria–helminth coinfections are prevalent among schoolchildren in rural Tanzania and the pattern varies between agro-ecosystems. Results of this study suggest that integrated control of malaria and helminthes should be designed based on the local agro-ecosystems.