Fungal plant pathogens secrete effector proteins to promote disease during infection of their host. Many of these are known to enter host cells and some have been found to target various subcellular compartments. Despite the identification of a large number of effectors from a wide variety of fungal plant pathogens, very little is known about the precise roles they play during infection, or the molecular mechanism that mediates effector-uptake into plant cells. Infections by biotrophic rust fungi constitute a major disease threat to agriculture, particularly for cereal crops in Australia. During infection, rusts produce specialised extensions called haustoria that penetrate the host cell walls while remaining surrounded by the host cell plasma membrane. The interaction between flax (Linum usitatissimum) and the flax rust fungus (Melampsora lini) is one of the best-characterised fungal pathosystems and has provided a strong basis for understanding rust resistance controlled by host resistance proteins in effector-triggered immunity. We have now isolated six flax rust effectors and all have been found to be small proteins secreted from haustoria and delivered into the host cytosol. We are using a number of techniques to understand their function during infection of a susceptible host, and to understand how they are able to enter host cells. Filling these gaps in our knowledge will give us a better understanding of the molecular mechanisms used by rust fungi to manipulate host plants to establish an infection, and may help develop novel disease resistance strategies to combat the devastating effects of rust disease.