Researchers from 13 EU nations analysed pollen levels for more than 20 species of tree and plant.
They found that many, including several that cause allergies such as hay fever, correlated with rising CO2 levels.
Presenting their study at the European Geosciences Union (EGU) annual meeting, scientists said city planners might need to review which trees they plant.
Hay fever and other allergies appear to be rising across Europe.
In the UK, GP diagnoses of allergic rhinitis, which includes hay fever, rose by a third between 2001 and 2005.
It has been suggested that higher temperatures might be causing plants to produce more pollen.
But by comparing pollen counts during relatively hotter and relatively cooler years, this latest study found temperature was not the cause.
Annette Menzel from the Technical University of Munich said other possible factors were eliminated as well.
"We thought the increase in the amount of pollen could be related to land use changes, but we don't observe this," she told BBC News.
"We tried to link it to temperature, but that's not possible.
"So the only effect that's left would be a CO2 effect; and we know from experiments in the real world and in climate chambers that CO2 does promote the amount of pollen [that trees produce]."Urban conundrum Continue reading the main story
The season of suffering for people with hay fever is getting more serious”End Quote Annette Menzel Technical University of Munich Data in the study came from pollen monitoring stations in the 13 nations, supplemented by tree cover information from the UN Food and Agriculture Organization and weather data.
Not all the 25 species studied show the same trend - pollen counts from some have actually gone down.
But 60% of species have seen an increase in pollen production across the decades of the study period, including nine species known to produce allergenic pollen.
There were also differences between trends in different countries, with pollen counts falling in a few.
Perhaps the most intriguing finding was that pollen counts have generally increased with CO2 inside cities, but not outside.
The researchers suggest this could be down to the longer lifetime of ozone molecules outside urban areas.Pollen causes inflammation of the air passages by stimulating the immune system
The gas is known to disrupt plant growth.
Although more research remains to be done, Professor Menzel's team suggests further rises in pollen counts probably lie ahead, given that CO2 concentrations are rising.
The increasing length of pollen seasons in Europe is linked to the introduction of plants and trees from other continents, in addition to any impact of CO2.
"In Germany, it is now only in November that we do not see allergenic pollen - so the season of suffering for people with hay fever is getting more serious," she said.
"On a local scale, planners should be more aware of what sort of problems may arise from the urban trees they're planting.
"Often they use birch trees, for example, because of their nice silver colour, not aware that they leave allergenic problems behind."
Many of the researchers on this project are involved in wider efforts to plot climate impacts on the timing of natural events such as plant flowering, egg laying and bird migration across Europe - the field of phenology.
The hay fever research presented at EGU will shortly be written up for formal scientific publication.
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