Among a large number of plant secondary metabolites, alkaloids comprise one of the most important groups due to their strong and divergent biological activities, and some are applied for clinical use. Alkaloids are often highly accumulated in particular organs of medicinal plants, which are called the ‘medicinal part’, whereas it is known that some alkaloids are translocated from source organs to such sink organs. The movement of biosynthetic intermediates from specific cells to other types of cells in tissue, and further detailed movement within the organelles in a cell is also suggested. However, little is known how alkaloids are transported across membranes and finally accumulated in specific organelles such as vacuole of the sink organ. To increase the productivity of valuable alkaloids in planta, not only biosynthetic genes of alkaloids but also genes involved in their transport will be important. Recently, the involvement of ABC transporters in the translocation of berberine alkaloid from root to rhizome was reported, while H+ antiporters were also suggested as the responsible transporters for vacuolar accumulation of the alkaloid. In this review, we describe intra-organ, intra-tissue and intra-cellular transport of the alkaloid via membrane transports. Furthermore, we discuss the possibility of increasing alkaloid production in transgenic plants by using alkaloid transporter genes.