To prioritize 100 animal diseases and zoonoses in Europe, we used a multicriteria decision-making procedure based on opinions of experts and evidence-based data. Forty international experts performed intracategory and intercategory weighting of 57 prioritization criteria. Two methods (deterministic with mean of each weight and probabilistic with distribution functions of weights by using Monte Carlo simulation) were used to calculate a score for each disease. Consecutive ranking was established. Few differences were observed between each method. Compared with previous prioritization methods, our procedure is evidence based, includes a range of fields and criteria while considering uncertainty, and will be useful for analyzing diseases that affect public health.