It has been previously shown that PPAR gamma ligands induce apoptotic cell death in a variety of cancer cells. Given the evidence that these ligands have a receptor-independent function, we further examined the specific role of PPAR gamma activation in this biological process. Surprisingly, we failed to demonstrate that MDA-MB-231 breast cancer cells undergo apoptosis when treated with sub-saturation doses of troglitazone and rosiglitazone, which are synthetic PPAR gamma ligands. Acridine orange (AO) staining showed acidic vesicular formation within ligand-treated cells, indicative of autophagic activity. This was confirmed by autophagosome formation as indicated by redistribution of LC3, an autophagy-specific protein, and the appearance of double-membrane autophagic vacuoles by electron microscopy following exposure to ligand. To determine the mechanism by which PPAR gamma induces autophagy, we transduced primary mammary epithelial cells with a constitutively active mutant of PPAR gamma and screened gene expression associated with PPAR gamma activation by genome-wide array analysis. HIF1 alpha and BNIP3 were among 42 genes up-regulated by active PPAR gamma. Activation of PPAR gamma induced HIF1 alpha and BNIP3 protein and mRNA abundance. HIF1 alpha knockdown by shRNA abolished the autophagosome formation induced by PPAR gamma activation. In summary, our data shows a specific induction of autophagy by PPAR gamma activation in breast cancer cells providing an understanding of distinct roles of PPAR gamma in tumorigenesis.