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The Fluidigm® CyTOF system is a mass cytometer that uniquely enables high-dimensional single-cell analysis of complex populations. Mass cytometry is based on inductively coupled plasma time-of-flight mass spectrometry used for multiplex proteomic analysis. In this approach, metal-conjugated affinity reagents are used to tag the components of cells. The cells are nebulized and sent to an argon plasma, ionizing the multi-atom metal tags, which are then analyzed by a time-of-flight mass spectrometer. Gene expression can be finely tuned through the synthesis of RNA and through the control of its stability and location. Misregulation of gene expression can have severe consequences, such as developmental disorders, cancer and autoimmune diseases. The ability to acquire complete spatial-temporal profiles of gene expression is therefore critical for the understanding of disease pathophysiology, medical diagnostics and drug discovery. In this presentation, we discuss the development of a multiplex method for targeted RNA detection using the Fluidigm CyTOF® and Advanced Cell Diagnostics RNAscope® platforms. This novel assay includes the hybridization of RNA-specific target probes, followed by signal amplification and ending with the binding of amplifier-specific metal-labelled probes. Presently, we are able to detect four different mRNA probes in a single-cell analysis setting. The detection of RNA is compatible with Fluidigm products such as Maxpar® antibodies. Future developments will include high-dimensional detection that enables researchers to investigate the simultaneous expression profile of RNA and protein across millions of cells.