High-throughput sequencing has allowed for unprecedented detail in gene expression analyses, yet its efficient application to single cells is challenged by the small starting amounts of RNA. We have developed CEL-Seq, a method for overcoming this limitation by barcoding and pooling samples before linearly amplifying mRNA with the use of one round of in vitro transcription. We show that CEL-Seq gives more reproducible, linear, and sensitive results than a PCR-based amplification method. We demonstrate the power of this method by studying early C. elegans embryonic development at single-cell resolution. Differential distribution of transcripts between sister cells is seen as early as the two-cell stage embryo, and zygotic expression in the somatic cell lineages is enriched for transcription factors. The robust transcriptome quantifications enabled by CEL-Seq will be useful for transcriptomic analyses of complex tissues containing populations of diverse cell types. Display omitted ► We present CEL-Seq, a single-cell transcriptomics method using in vitro transcription ► We show that CEL-Seq is linear, sensitive, and reproducible ► CEL-Seq is highly multiplexed, allowing for the parallel examination of hundreds of cells ► We describe early C. elegans embryology at the single-cell transcriptomic level Yanai and colleagues have developed CEL-Seq, an RNA-Seq method for assaying the transcriptome at the single-cell level. CEL-Seq works by barcoding and pooling dozens of samples before linearly amplifying mRNA using one round of in vitro transcription. We show that CEL-Seq gives highly reproducible, linear, and sensitive results. We demonstrate the power of this method by studying early C. elegans embryonic development at single-cell resolution.