As birch pollen allergen enters epithelium of allergic patients via lipid rafts and caveola we began to analyse its putative amphiphilic and lipid ligands on atomic level using molecular modelling and computational ligand docking. We carry out 3D modelling docking with both experimentally verified Bet v 1 ligands as well as larger lipid molecules for which experimental affinity studies were not available. The results suggest that the hydrophobic cavity of Bet v 1 has different binding sites for different ligands and groups of ligand type-specific amino acids can be defined. Bet v 1 proteins may also be able to bind and transport more complex amphiphilic molecules like ceramides and sphingomyelins known to be enriched on caveolae/lipid rafts. Furthermore, the suggested binding mode, where the hydrophobic tail groups of lipids locate inside Bet v 1, while the polar head group may remain solvent accessible, would allow Bet v 1 to bind glycolipids, e.g. gangliosides, also rich on caveolae/lipid rafts. Taken together, this in silico work suggests that Bet v 1 bind to amphiphilic and lipid ligands present on the caveolae/lipid rafts and thus could provide a molecular mechanism for the pollen entry to epithelial tissue of allergic patients.