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Introduction: Lymphatic filariasis (LF) and malaria are two vector-borne diseases which parasites can simultaneously infect human or mosquito. In Burkina Faso, studies mainly focused on the control of these diseases independently. Hence, there is a lack of information on their co-transmission of to both human and vector. The present study aimed at providing baseline data from endemic areas in Burkina Faso towards a successful integrated management of both diseases. Methods: The study was carried out in six sites distributed in the East, Center-East and South-West regions of Burkina Faso. Data were collected in August 2014 and September 2015. The infection rates in human and vector populations, vector diversity, trophic and resting behavior were investigated. To determine the disease prevalence nocturnal finger- prick blood sample and microscopic observations were performed. Vectors collected by human landing catches and pyrethrum spray collections. Biochemical and molecular analyses were performed to identify Anopheles gambiae sensu lato sibling species, and to determine vector infection rate and their blood meal origins. Results: Results indicate residual transmission of LF and malaria in human and vector populations. A low co-infection rate (Wuchereria bancrofti and Plasmodium falciparum was noted in both human and mosquito. Anopheles gambiae s.l. , An. funestus s.l. and An. nili were by order the main potential vectors encountered. It was in majority parous females and exhibited endophagic and exophagic behavior. Parasite’s co-infection was found with An. coluzzii and An. nili only. Conclusion: The present study has provided basic information on the (co-)transmission of both diseases in the study areas. These results will be useful for further investigations towards the development and implementation of a better integrated strategy to control these diseases.