Analysis of the transcriptomes of single cells can provide a comprehensive understanding of the heterogeneous expression and gene regulatory networks within a population of cells. Through mRNA isolation, reverse transcription, amplification and deep-sequencing analysis, the transcriptional landscape can be obtained for subsequent detailed quantitative investigation of the levels and variation of gene expression underlying the relationship between the genotype and phenotype of a single cell. Not surprisingly, it has been applied within many fields such as developmental biology, basic medicine, clinical research and drug discovery. This review introduces the history, progress, and technological characteristics of whole transcriptome analyses of single cells, as well as detailed strategies and advantages of the methodology. The technical challenges, potential applications, and future developments are also discussed.