Elevated levels of IL-1β are known to induce apoptosis in pancreatic β-cells potentially through ER (endoplasmic reticulum) stress induction and subsequent c-jun-N-terminal kinase 1/2 (JNK1/2) activation. In an earlier report, we had demonstrated JNK1/2 activation to be initiated prior to ER stress and apoptotic induction in response to IL-1β. However, the detailed regulatory mechanisms of these phenomena are not yet completely understood. Since the ER is identified as the organelle responsible for Ca(2+) handling and storage; in this article, we sought to elaborate on the consequent effects of IL-1β on cellular Ca(2+) movements and mitochondrial dysfunction and to evaluate the role of JNK1/2 herein. Our results show that in RIN5mF cells and in human primary β-cells, IL-1β alters mitochondrial membrane potential, mPTP opening, ATP content and ROS production and these alterations were preceded by ER Ca(2+) release via IP3R channels and by mitochondrial Ca(2+) uptake. All these events were prevented by JNK1/2 siRNA indicating the mediatory role of JNK1/2 during IL-1β induced cellular alterations. This was accompanied by IL-1β induced apoptosis that was prevented by JNK1/2 siRNA and the IP3R inhibitor, Xestospongin C. These suggest a regulatory role of JNK1/2 toward modulation of the ER-mitochondrial-Ca(2+) axis by IL-1β during apoptotic cell death.