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Introduction: Onchocerciasis is a chronic neglected tropical disease caused by the filarial nematode Onchocerca volvulus, which is endemic in Equatorial Guinea. The aim was to estimate the current spatial distribution of onchocerciasis, and its related factors, in Bioko Island after several years of mass drug administration and vector control activities, by using GIS technics. Methodology: The survey was carried out within the framework of a wider research project entitled "Strengthening the National Programme for Control of Onchocerciasis and other Filariasis in Equatorial Guinea". A structured questionnaire was designed to cover basic sociodemographic information and risk factors for onchocerciasis and the coordinates of household. the hydrographic network data to calculate the positive onchocerciasis rate was used. Poisson generalized linear model was used to explore the association between onchocerciasis and the following covariates: distance to the river, preventive practices, water source and househol'ds main source of income. Two different cluster analysis methods were used: Getis-Ord Gi statistic and SaTScan™ purely spatial statistic estimator. Results: The risk of onchocerciasis was higher for those who drank water from external sources (RR 25.3) than for those who drank home tap water (RR 8.0). The clusters with z-score higher were located at the east of the island. For 5 km and 1 km distances, one significant cluster in the east was detected (RR 5.91 and RR 7.15). Conclusion: No environmental factors related with onchocerciasis were found, including proximity to rivers. This could be partially explained by the fact that the vector was eliminated in 2005. [ABSTRACT FROM AUTHOR]