The great majority of seed proteins that are stored in the vacuole prior to desiccation are transported via the Golgi apparatus. In this organelle they are separated from other products of the secretory pathway. Evidence is accumulating that the mechanism for segregation of storage proteins is different from that of soluble proteins destined for lytic vacuoles: it rarely seems to require short targeting propeptides at the N- or C-terminus. Instead, the three-dimensional conformation of the protein appears to be a critical factor, leading to self-assembly into osmiophilic aggregates. Also unusual is that this process starts immediately after entry into the Golgi apparatus, i.e. at the cis-cisternae, rather than at the trans-pole where acid hydrolases are packaged into clathrin-coated vesicles. Storage protein aggregates accumulate into so-called “dense” vesicles at the periphery of the cisternae and are transported towards the trans-pole of the Golgi apparatus by cisternal progression. Before the dense vesicles are released, clathrin-coated vesicles form at their surface; however, the function of the latter remains the object of speculation. In other eukaryotes, delivery of Golgi-derived lumenal products to the vacuole does not occur directly, but via a pre-vacuolar compartment. There is evidence that this is also the case for plants, and in developing pea cotyledons the pre-vacuolar compartment takes the form of a large multivesicular body. Ultimately this appears to fuse in toto with the protein storage vacuole.