Perturbation of the circadian clock is a risk factor for metabolic diseases. Beta-Cell specific clock disruption causes glucose intolerance in mice, associated with oxidative stress and secretory failure in beta-cells. Proinflammatory cytokines alter the expression of core-clock machinery in human and rodent beta-cells, but the molecular mechanisms and consequences for cell viability are unclear. We hypothesized that cytokine-mediated clock perturbation in beta-cells is NF-kappaB driven, concomitant with cytokine-induced apoptosis, and depends on the cellular synchronization status. Cytokine-mediated changes of core-clock mRNA expression observed in non-synchronized INS-1 cells were potentiated in synchronized cells. These transcriptional changes differentially translated into alterations in core-clock protein levels. Interestingly, synchronization also sensitized INS-1 cells to cytokine-mediated cytotoxicity, associated with potentiation in the expression of inducible (ind) proteasomal catalytic subunits, ER stress markers, NF-kappaB activity, and activation of the intrinsic apoptotic pathway. Small-molecule NF-kappaB inhibition abrogated cytokine-mediated regulation of clock gene expression in both synchronized and non-synchronized INS-1 cells and reversed cytokine-mediated alterations in circadian parameters in INS-1 reporter cells at non-cytotoxic concentrations. However, at cytotoxic cytokine concentrations, NF-kappaB inhibition caused a loss of circadian rhythmicity while still reducing the cytotoxic effects of cytokines, indicating a differential effect of NF-kappaB signaling in controlling beta-cell viability and clock regulation. We propose that in synchronized cells, the proinflammatory transcriptional activity of NF-kappaB is enhanced by interaction with clock transcription factors, as has been suggested for the clock activator Brain and muscle Arnt-like protein-1 (Bmal1). Thus, desynchronization provides a novel anti-apoptotic defense mechanism in response to cytokine assault, similar to that provided by beta-cell phenotypic de-differentiation.