In Puerto Rico, respiratory diseases affect a significant percentage of the population, and it is possible that the environmental factors unique to the island, such as easterly winds, dense vegetation, and high humidity, may increase the concentration of airborne biological particulates that could distress susceptible individuals. As most studies characterized fungal spores and pollen in temperate zones, we wanted to describe their concentrations in a tropical zone. The Allergenco Ò (MK3) spore trap was used to monitor airborne spores and pollen concentrations for 12 months starting on May 2005. During the length of the study, silicone grease-coated microscope slides captured 12 impacts daily, which were then stained with calcofluor and observed under the microscope with bright field and ultraviolet light. Atmospheric conditions were recorded with the Precision Weather Station Ò . Precipitation, dew point, and relative humidity promote the presence of fungal spores in San Juan throughout the year, with basidiospores being the most frequent. Spore concentrations were higher during the early morning hours all the year around. Wind and gusts were dispersal factors, and humidity and the dew point favored the release of spores into the atmosphere. In contrast to spores, pollens were not found to be affected by any of the meteorological factors and no distinctive patterns were found. Describing how airborne spores and pollens, many of which have allergenic potential, behave in the tropics, such as in San Juan, Puerto Rico, could be used to design preventive measures for the benefit of the sensitized population. Information about the presence and abundance of aeroallergens will assist in the diagnosis of allergic rhinitis and asthma on the island.