Despite the existence of antiamaril vaccine in the routine Expanded Program of Immunization (EPI) in Burkina Faso, yellow fever cases still occur in the country. In collaboration with WHO, the national health authorities set up a surveillance system through the national reference laboratory in Centre Muraz (Bobo-Dioulasso). All samples of feverish icterus cases of the 63 health districts of the country were analysed in this lab for M Immunoglobulin using Enzyme Linked Immunosorbent Assay (Elisa). Positive Elisa samples were sent to Pasteur Institute of Dakar (Senegal) for confirmation using a Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) assay. From 2003 to 2005, the number of confirmed cases of yellow fever was respectively of 1/413 (0.24%), 14/616 (2.27%) and 19/618 (3.07%). This increasing of the proportion was statistical different. Then, from 2006 to 2008, the confirmed case proportion was respectively 0.35%, 0.27 and 0.54% without significant difference (P = 0.69). The entomological investigations conducted in 2004 in Bobo-Dioulasso showed that the water pots constitute 48.11% mosquitoes lodgings, followed by metal drums with a strong representation of Culex quinquefasciatus (48.7%), followed by Aedes aegypti (43.3%), as vectors in domestic areas with sectorial variations. These results suggest that more attention must be paid by the national health authorities and international community regarding this disease.