Objective:To analyze lncRNA expression profiles in MIN6 cells,which belong to mouse pancreatic β cells, exposed to cytokines (IL-1β, TNF-α and IFN-γ) and to perform preliminary validation. Methods: MIN6 cells were incubated in the presence or absence of the cytokines mentioned aboved for 24 h. Cell apoptosis was detected by flow cytometry and cell viability was assessed using the Cell Counting kit-8. Affymetrix GeneChip Mouse Transcriptome Array 1.0 was performed to identify differently expressed lncRNA and mRNA in MIN6 cells exposed to cytokines compared with the normal control group. The interesting candidate lncRNAs were verified by Real-time quantitative PCR. Results: Cytokines promoted MIN6 cells apoptosis and inhibited the viability of MIN6 cells. A total of 723 differently expressed lncRNAs were identified in the cytokine-stimulated group compared with the control group with a set filter fold-change ≥ 2.0, of which 444 upregulated and 279 downregulated. Additionally, 111 differently expressed lncRNAs were identified with a set filter fold-change ≥ 5.0, of which 105 upregulated and 6 downregulated. And 2 180 differently expressed mRNAs were identified with a set filter fold-change ≥ 1.5. We also found, via quantitative PCR, that 10 lncRNAs were aberrantly expressed in the cytokine-stimulated group compared with the control group. The results of the qRT-PCR were consistent with the data from the microarray. Conclusion: The results revealed that there are differently expressed lncRNAs in MIN6 cells exposed to cytokines compared with the control group. These lncRNAs may play a key role in cytokine-induced apoptosis of pancreatic β cells.