RNA trafficking and localization are important processes that influence cellular physiology at the epigenetic, post-transcriptional, and post-translational levels. Conventional techniques such as qRT-PCR and DNA microarrays are cell lysate-based assays that provide ensemble averages of RNA expression levels. To improve our current understanding of the role of RNAs in health and disease, there is great interest among RNA biologists to visualize individual RNAs in cells. There are currently three popular approaches — fluorescence in situ hybridization (FISH), the MS2 system, and molecular beacons (MBs) — commonly employed by researchers to study RNAs at the single-molecule level in various cellular contexts. Below, we discuss each technique’s usage, advantages, and limitations.