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Recent developments of single cell transcriptome profiling methods have led to the realization that many seemingly homogeneous cells have surprising levels of expression variability. The biological implications of the high degree of variability is unclear but one possibility is that many genes are restricted in expression to small lineages of cells, suggesting the existence of many more cell types than previously estimated. Noncoding RNA(ncRNA) are thought to be key parts of gene regulatory processes and their single cell expression patterns may help to dissect the biological function of single cell variability. Technology for measuring ncRNAin single cell is still in development and most of the current single cell datasets have reliable measurements for only long noncoding RNA (lncRNA). Most works report that lncRNAsshow lineage‐specific restricted expression patterns, which suggest that they might determine, at least in part, lineage fates and cell subtypes. However, evidence is still inconclusive as to whether lncRNAsand other ncRNAsare more lineage‐specific than protein‐coding genes. Nevertheless, measurement of ncRNAsin single cells will be important for studies of cell types and single cell function. WIREs RNA2017, 8:e1433. doi: 10.1002/wrna.1433 For further resources related to this article, please visit the WIREs website. Single cell transcriptome analysis reveals cell‐to‐cell variability in noncoding RNA expression