Involvement of dysregulated autophagy in cancer growth and progression has been shown in different tumour entities, including pancreatic ductal adenocarcinoma (PDA). PDA is an extremely aggressive tumour characterized by a small population of highly therapy‐resistant cancer stem cells (CSCs) capable of self‐renewal and migration. We examined whether autophagy might be involved in the survival of CSCs despite nutrition and oxygen deprivation typical for the hypoxic tumour microenvironment of PDA. Immunohistochemistry revealed that markers for hypoxia, CSCs and autophagy are co‐expressed in patient‐derived tissue of PDA. Hypoxia starvation (H/S) enhanced clonogenic survival and migration of established pancreatic cancer cells with stem‐like properties (CSC ^high), while pancreatic tumour cells with fewer stem cell markers (CSC ^low) did not survive these conditions. Electron microscopy revealed more advanced autophagic vesicles in CSC ^high cells, which exhibited higher expression of autophagy‐related genes under normoxic conditions and relative to CSC ^low cells, as found by RT‐PCR and western blot analysis. LC3 was already fully converted to the active LC3‐II form in both cell lines, as evaluated by western blot and detection of accumulated GFP‐LC3 protein by fluorescence microscopy. H/S increased formation of autophagic and acid vesicles, as well as expression of autophagy‐related genes, to a higher extent in CSC ^high cells. Modulation of autophagy by inhibitors and activators resensitized CSC ^high to apoptosis and diminished clonogenicity, spheroid formation, expression of CSC‐related genes, migratory activity and tumourigenicity in mice. Our data suggest that enhanced autophagy levels may enable survival of CSC ^high cells under H/S. Interference with autophagy‐activating or‐inhibiting drugs disturbs the fine‐tuned physiological balance of enhanced autophagy in CSC and switches survival signalling to suicide. Copyright© 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.