The evaluation of genetically modified (GM) plants under special screened greenhouse conditions is the first step of assessing the risks of pollen dispersal from GM plants. To obtain fundamental information on the effective use of special screened greenhouses, we examined the pollen grain sizes of the major plants used for transgenic studies in Japan to estimate the effective fine-mesh size for covering the openings of special screened greenhouses to reduce pollen dispersal. Second, we examined the potential of small insects as possible pollen vectors. Finally, we investigated the relationship between fine-mesh size and air temperature in a covered space using a model of a special screened greenhouse. Although using smaller mesh sizes for covering the openings was clearly more effective in reducing pollen dispersal, the smaller mesh raised the air temperature substantially and resulted in poorer growing conditions for plants. We discuss this dilemma and suggest conclusions based on our research.