Many biological phenomena are either invisible or only partially characterized when interrogated using standard analyses that average data across a bulk population of cells. Now, technological advances are providing unprecedented opportunities to analyse the complexities of biological systems at the single-cell level. High-throughput analyses of the genomes, transcriptomes and proteomes of single cells are yielding novel and important insights into diverse processes such as development, gene-expression dynamics, tissue heterogeneity and disease pathogenesis. In this Focus issue, we highlight the transformative potential of single-cell omics approaches.