Technical innovations in the last decade have allowed to sequence transcriptomes of single cells. Single-cell RNA-sequencing (scRNA-seq) has since then opened the window to a deeper understanding of cellular identity and is becoming a widely used method in molecular biology. In neuroscience, scRNA-seq has broad applications, for example in determining cellular diversity in different brain regions and in revealing transcriptomic variations across brain disorders. The method consists of several steps: isolation and lysis of single cells, reverse transcription of RNAs, amplification of cDNAs, and next-generation sequencing. The large datasets can subsequently be analysed using different bioinformatic tools to deduce biological meaning. Current developments aim to integrate scRNA-seq into cellular network analysis through multimodal analysis, spatial localisation and perturbation experiments, in order to understand brain physiology and pathology.