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Background: Lymphatic filariasis (LF) is still a public health burden in many developing countries. In Benin, a West African country, at least 6.6 million people are at risk for LF. With the goal of eliminating LF by 2020, mass drug administration (MDA) has been scaled-up during the last decade. Currently, 23 districts are believed to have eliminated LF as a public health problem, and 25 other districts are still under treatment. In this study we report the results of the first transmission assessment survey of LF (TAS1) in 13 districts from the second group, which have received at least six rounds of MDA with albendazole and ivermectin., Methods: The 13 districts were grouped into six evaluation units (EU). In each EU, 30 schools randomly selected by survey sample builder (SSB) software were surveyed. Children aged six and seven were sampled in schools and for each child the Alere™ Filariasis Test Strip test was carried out using finger-prick blood to detect the circulating filarial antigen from Wuchereria bancrofti., Results: Overall, 9381 children were sampled in 191 schools from the six EU with 47.6% of the children aged six years and 52.4% aged seven years. Five EU passed the assessment, with no positive cases identified. The EU of Ouinhi which grouped the districts of Ouinhi, Cove, Za-Kpota and Zagnanado failed, with 47 positive cases. These cases were clustered in the districts of Ouinhi (n = 20), Za-Kpota (n = 11) and Zagnanado (n = 16). No cases were found in the district of Cove., Conclusions: The findings of our study indicate that Benin has made important progress towards elimination in most districts evaluated. However, this study also shows that transmission of LF is ongoing in the EU of Ouinhi, part of the Zou department. The MDA strategy needs to be strengthened in order to control the human reservoir of infection in these districts.