SummaryWe present a protocol to detect cells that have been infected by RNA viruses. The method, RNA fluorescencein situhybridization flow cytometry (RNA FISH-Flow), uses 48 fluorescently labeled DNA probes that hybridize in tandem to viral RNA. RNA FISH-Flow probes can be synthesized to match any RNA virus genome, in either sense or anti-sense, enabling detection of genomes or replication intermediates within cells. Flow cytometry enables high-throughput analysis of infection dynamics within a population at the single cell level.For complete details on the use and execution of this protocol, please refer to Warren et al. (2022).1