In 2013, Benin developed strategies to control neglected tropical diseases and one of the first step was the disease mapping of the entire country in order to identify endemic districts of schistosomiasis and soil transmitted helminths (STH). This study was carried out in 30 of the 77 districts of Benin. Of these 30 districts 22 were previously treated for Lymphatic Filariasis (LF) using the Ivermectin and Albendazole combination. In each district, five schools were selected and 50 children aged 8 to 14 years were sampled in each school, making a total of 250 children sampled in the district. The schools were selected mainly according to their proximity to lakes or any bodies of water that were likely to have been used by the children. Samples of faeces and urine were collected from each pupil. Urinary schistosomiasis was identified using the urine filtration technique while STH and intestinal schistosomiasis were identified through the Kato Katz method. Overall a total of 7500 pupils were surveyed across 150 schools with a gender ratio of 1:1. Hookworm was identified in all 30 districts with a prevalence ranging from 1.2% (95%CI: 0.0-2.5) to 60% (95%CI: 53.9-66.1). Ascaris lumbricoides was detected in 19 districts with a prevalence rate between 1% (95%CI: 0.0-2.2) and 39% (95%CI: 32.9-45.0). In addition to these common STH, Trichuris trichiura, Enterobius vermicularis and Strongyloides stercoralis were found at low prevalence. Only 16 districts were endemic to Schistosoma mansoni, while 29 districts were endemic to S. haematobium. The S. haematobium prevalence ranged from 0.8% (95% CI: 0.0-1.9) to 56% (95% CI: 50.2-62.5) while the prevalence of S. mansoni varied from 0.4% (95%CI: 0.0-1.2) to 46% (95% CI: 39.8-52.2). The 22 districts, where LF was successfully eliminated, still require mass drug administration (MDA) of albendazole indicating that school-based MDA would be needed even after LF elimination in districts co-endemic to LF and STH in Benin.