Despite recent National Immunization Days in Burkina Faso, the rural province of Houët reported >400 measles cases in 2001 (82% not vaccinated). Phylogenetic analysis of 58 measles virus field isolates plus the first sequences from the Democratic Republic of the Congo and the Republic of Congo are reported. All viruses were genotype B3, which is common in the region. In Houët, there were two geographically confined genetic variants, suggesting two independent importation events. Strain diversity in Houët (1.5%) and the Congos was limited in comparison with Ibadan, Nigeria (4.6%), where measles is endemic. Strain variability, assessed by heteroduplex mobility assay, confirmed these findings. Despite large local pools of susceptible persons even after several rounds of vaccination, the limited strain diversity suggests that parts of rural Burkina Faso may be moving from an endemic to an epidemic transmission pattern of measles virus.