Autophagy is an intracellular bulk protein degradation system. Beclin is known to be involved in this process; however, its role is unclear. In this study, we showed that Beclin was co‐immunoprecipitated with phosphatidylinositol (PtdIns) 3‐kinase, which is also required for autophagy, suggesting that Beclin is a component of the PtdIns 3‐kinase complex. Quantitative analyses using a cross‐linker showed that all Beclin forms a complex with PtdIns 3‐kinase, whereas∼ 50% of PtdIns 3‐kinase remains free from Beclin. Indirect immunofluorescence microscopy demonstrated that the majority of Beclin and PtdIns 3‐kinase localize to the trans‐Golgi network (TGN). Some PtdIns 3‐kinase is also distributed in the late endosome. These results suggest that Beclin and PtdIns 3‐kinase control autophagy as a complex at the TGN.