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The impact of allergens emitted by urban green spaces on health is one of the main disservices of ecosystems. The objective of this work is to establish the potential allergenic value of some tree species in urban environments, so that the allergenicity of green spaces can be estimated through application of the Index of Urban Green Zones Allergenicity (IUGZA). Multiple types of green spaces in Mediterranean cities were selected for the estimation of IUGZ. The results show that some of the ornamental species native to the Mediterranean are among the main causative agents of allergy in the population; in particular, Oleaceae, Cupressaceae, Fagaceae, and Platanus hispanica. Variables of the strongest impact on IUGZA were the bioclimatic characteristics of the territory and design aspects, such as the density of trees and the number of species. We concluded that the methodology to assess the allergenicity associated with urban trees and urban areas presented in this work opens new perspectives in the design and planning of urban green spaces, pointing out the need to consider the potential allergenicity of a species when selecting plant material to be used in cities. Only then can urban green areas be inclusive spaces, in terms of public health.