The cultivation of genetically modified (GM) crops has raised in the European Union and other parts of the world numerous concerns about their environmental and economic impact. Especially outcrossing of genetically modified organisms (GMO) was from the beginning a critical issue as airborne pollen has been considered an important way of GMO dispersal. Here, we investigate the use of airborne pollen sampling combined with microscopic analysis and molecular PCR analysis as an approach to monitor GM maize cultivations in a specific area. Field trial experiments in the European Union and South America demonstrated the applicability of the approach under different climate conditions, in rural and semi-urban environment, even at very low levels of airborne pollen. The study documents in detail the sampling of GM pollen, sample DNA extraction and real-time PCR analysis. Our results suggest that this ''GM pollen monitoring by bioaerosol sampling and PCR screening" approach might represent an aid in managing the co-cultivation of GM and non-GM crops, especially in the surveillance of GM-free areas, centres of origin, and natural reserves.