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The male seminal fluid contains factors that affect female post‐mating behavior and physiology. In Drosophila, most of these factors are secreted by the two epithelial cell types that make up the male accessory gland: the main and secondary cells. Although secondary cells represent only ~4% of the cells of the accessory gland, their contribution to the male seminal fluid is essential for sustaining the female post‐mating response. To better understand the function of the secondary cells, we investigated their molecular organization, particularly with respect to the intracellular membrane transport machinery. We determined that large vacuole‐like structures found in the secondary cells are trafficking hubs labeled by Rab6, 7, 11 and 19. Furthermore, these organelles require Rab6 for their formation and many are essential in the process of creating the long‐term postmating behavior of females. In order to better serve the intracellular membrane and protein trafficking communities, we have created a searchable, online, open‐access imaging resource to display our complete findings regarding Rab localization in the accessory gland. The secondary cells of the Drosophila male accessory gland are a polarized, secretory cell‐type required for optimal male fertility. These cells are filled with large vacuole‐like compartments (VLCs) that are labeled by combinations of four Rab‐GTPases (Rab6, 7, 11 and 19). Secretory markers localize within VLCs marked by Rabs6, 11 and sometimes 19, suggesting a role for these compartments in secretion. Although the VLC differ in function and importance in reproduction, they are all derived from a common Rab6 compartment within the hours after adult eclosion. [ABSTRACT FROM AUTHOR]