Exposure to allergens represents a key factor among the environmental determinants of asthma. The most common information available for pollinosis patients is the concentration of pollen grains in the bioaerosol and their temporal distribution. However, in recent years, discordance between pollen concentrations and allergic symptoms has been detected. The purpose of this research is to evaluate the relationship between pollen counts and the atmospheric aeroallergen concentrations in different Spanish bioclimatic areas. For the monitoring of allergen content in the air, a quantitative antigen-antibody technique combined with the Cyclone sampling methodology was used. The study was conducted during 2007 by considering some of the most common allergens that induce pollinosis in each area: Platanus and Urticaceae in Ourense and Cartagena, and Poaceae in Ourense and León. In Ourense, pollen counts and aeroallergen concentrations coincided for the three pollen types studied, and the pollen and allergen data associated with the meteorological factors were highly significant for the pollen counts. In Cartagena (for Platanus and Urticaceae) and León (for Poaceae), the low correlations between pollen counts and allergen concentrations obtained could be due to the specific bioclimatic conditions. In contrast, the higher allergen concentrations found in the atmosphere in Cartagena and León compared to Ourense could be related to the existing pollutant levels there, inducing a higher expression of plant pathogenesis-related proteins in the plants of polluted cities. The combination of pollen counts and allergen quantification must be assessed to reliably estimate exposure of allergic people to allergens in different bioclimatic areas.