Apoptosis plays a critical role in the maintenance of gut mucosal homeostasis and is highly regulated by numerous factors including polyamines. Decreasing cellular polyamines promotes the resistance of intestinal epithelial cells (IECs) to apoptosis by increasing Akt kinase activity, but the exact mechanisms by which polyamine depletion activates Akt remain unknown. 3-phosphoinositide-dependent protein kinase-1 (PDK1), functions as a downstream of phosphatidylinositol-3 kinase (PI3K) and upstream of Akt and serves as a major regulator of Akt activity. The current study determined if polyamines regulate Akt activity by altering PDK1. Studies were conducted in IEC-6 cells, derived from rat small intestinal crypts. Depletion of cellular polyamines induced PDK1 phosphorylation and increased its kinase activity, which were prevented by exogenous polyamine putrescine. Induced PDK1 activation following polyamine depletion was associated with an increase in phosphorylated Akt (pAkt) and Akt kinase activity. In contrast, polyamine depletion did not alter levels of total PDK1 and Akt proteins. PDK1 silencing in polyamine-deficient cells not only prevented the induced Akt activation but also blocked the increased resistance to apoptosis. These results indicate that polyamine depletion enhanced Akt phosphorylation by increasing PDK1 kinase activity, thereby protecting IECs against apoptosis.