The objective of this study was to identify environmental characteristics of European Ramsar wetlands, which are natural habitats for waterbirds, that could have contributed as risk factors for H5N1 HPAI (highly pathogenic avian influenza) in water birds (2006–2009). Ramsar wetlands in which H5N1 outbreaks were reported were considered infected (positive), and a case-control study was conducted using a logistic regression model in order to identify environmental risk factors associated with disease. Forestry (odds ratio, OR = 6.90) and important area for water birds with mixosaline water (OR = 6.31), as well as distance to the nearest positive wetland (OR = 0.66), which was included into the model to adjust for spatial dependence, were associated with status of the wetlands. The model was used to estimate the risk for H5N1 HPAI on each European Ramsar wetland. Results will help to identify wetlands at high risk for H5N1 HPAI infection, wetlands that could be selectively targeted as part of a surveillance program aimed at early detection and prevention of future H5N1 HPAI epidemics.