Background: Urbanization is a main trend in developing countries and leads to health transition. Although non-communicable diseases are increasing in cities of low-income countries, vector-borne diseases such as malaria, are still present. In the case of malaria, transmission is lower than in rural areas, but is uneven and not well documented. In this study, we wanted to evaluate intra-urban malaria transmission in a West African country (Burkina Faso). Methods: A cross-sectional study on 847 adults (35 to 59 year-old) and 881 children (6 months to 5 year-old) living in 1045 households of four districts (Dogona, Yeguere, Tounouma and Secteur 25) of Bobo-Dioulasso was performed between October and November 2013. The districts were selected according to a geographical approach that took into account the city heterogeneity. Malaria prevalence was evaluated using thick and thin blood smears. Human exposure to Anopheles bites was measured by assessing the level of IgG against the Anopheles gSG6-P1 salivary peptide. Adult mosquitoes were collected using CDC traps and indoor insecticide spraying in some houses of the four neighbourhoods. The Anopheles species and Plasmodium falciparum infection rate were determined using PCR assays. Results: In this study, 98.5% of the malaria infections were due to Plasmodium falciparum. Malaria transmission occurred in the four districts. Malaria prevalence was higher in children than in adults (19.2 vs 4.4%), and higher in the central districts than in the peripheral ones (P = 0.001). The median IgG level was more elevated in P. falciparum-infected than in non-infected individuals (P < 0.001). Anopheles arabiensis was the main vector identified (83.2%; 227 of the 273 tested mosquito specimens). Five P. falciparum-infected mosquitoes were caught, and they were all caught in the central district of Tounouma where 28.6% (14/49) of the tested blood-fed mosquito specimens had a human blood meal. Conclusions: This study showed that urban mala