'Drop-seq' is a droplet-based, microfluidic method that allows the transcriptional profiling of thousands of individual cells, in a highly parallel and cost-effective way. A critical and often limiting step is the preparation of cells in an unperturbed state, not compromised by stress or ageing. This can be particularly challenging during prolonged handling or transport, or when cells are rare and need to be collected over several days. Here, we tested whether chemical fixation can be used to overcome these problems. Methanol fixation allowed us to stabilize and preserve dissociated cells for several weeks. Fixed cells contained intact RNA and enabled high quality cDNA library generation. By using mixtures of fixed human and mouse cells, we showed that individual transcriptomes could be confidently assigned to one of the two species. Single-cell gene expression measurements from live and fixed samples were highly correlated with each other and with bulk mRNA-seq data. We expect that the availability of a simple cell fixation method will open up many new opportunities to quantitatively analyze transcriptional dynamics at single-cell resolution. As an additional resource, we provide 'dropbead', an R package for easy exploration and quantitative evaluation of informative parameters in Drop-seq data.