Relationships between meteorological factors and airborne pollen concentrations at high altitudes are virtually unknown. We used cross-correlation analyses to test the relationships between daily variation in meteorological factors (i.e. temperature, humidity and wind speed) and airborne pollen concentration, diversity (number of families and Shannon and Simpson diversity indices) and evenness (Pielou index) in an Apennine high-altitude site (Gran Sasso Massif, 2117 m elevation). In contrast to patterns observed at low altitudes, the temperature had a negative correlation with pollen abundance and diversity, whereas humidity had a positive correlation. The unexpected negative correlations with temperature can be explained with the particular position of our sampling site. Wind speed was positively correlated with pollen diversity and abundance in the short term, which can be explained by the fact that higher wind speed promotes both primary emission of pollen from the anthers and subsequent re-suspension. Evenness and wind speed were negatively correlated in the short term because of the different response of different species to meteorological conditions. In the longer term, the average concentrations of the various taxa tend to reach similar values, leading to increased values of diversity. Our finding of a decrease in pollen emission with increasing temperature has important implications for the study of the impacts of global change on high-altitude plant communities. We also detected a high abundance of Cupressaceae/Taxaceae pollen, a reflection of the expansion of thermophilic species, such as Juniperus, due to climate change.