There are no current commercial releases of genetically modified white clover, but several research groups are working on traits such as virus resistance, stress tolerance and bloat safety that are likely to provide large economic benefits for livestock farmers. However, white clover pollen is a common constituent of honey produced by bees foraging white clover flowers. Therefore, there is a need to develop tools to detect the presence of genetically modified pollen in white clover honey. The results presented in this paper describe the development and application of PCR-based techniques to detect the Alfalfa mosaic virus coat protein gene (AMV CP) and the neomycin phosphotransferase 2 selectable marker gene (npt2) in genetically modified white clover pollen, whether this pollen is collected fresh, from honey bees that have been foraging white clover, or from honey. Further research and development will be required to develop ‘field-ready’ tools for the detection and quantification of these transgenes in pollen and honey products. However, this paper demonstrates prospects and principles in pollen and honey from honeybees foraging transgenic white clover.