Estimates were produced for onchocerciasis all-age microfiladermia (positive skin snip) prevalence at the 5x5 km-level in 34 endemic countries across Africa, plus Yemen, annually between 2000 and 2018. These estimates were produced using reported data on onchocerciasis prevalence from endemicity mapping surveys, surveillance during elimination programs, and other sources. This dataset includes the following: GeoTIFF raster files for pixel-level estimates of onchocerciasis prevalence CSV files of aggregated estimates of onchocerciasis prevalence for each country at the national level, and for first and second administrative divisions Code files used to generate the estimates