Monitoring gene expression is at the center of research for a wide variety of medical, biological, and biotechnological applications. Currently no method exists for true multiple gene expression monitoring inside of a single living cell that allows for the gene expression profile of the cell to be directly compared with another single living cell. By microinjecting multiple molecular beacons with different fluorophores inside of single breast carcinoma cells and monitoring with advanced fluorescent microscopy, the expression of multiple genes can be simultaneously monitored inside single living cells. Using ratiometric analysis as a basis for the measurements allows the different gene expression levels to be compared from cell to cell. Not only does this allow differentiation of individual mRNA expression levels between multiple single cells but it also allows for mRNA expression trend analysis at the single cell level.