Visualizing how signals are transmitted within a living cell has long been a goal of molecular biologists, which has now been realized by probes based on the principle of fluorescence resonance energy transfer (FRET). Variants of green fluorescent protein (GFP) enabled the preparation of genetically-encoded FRET probes, and their application has been expanded for use in many areas of biology. The GFP-based FRET probes can be classified as belonging to one of two types, intermolecular and intramolecular FRET probes. The merit of the intermolecular FRET probe lies in the ease of preparation of the probes, whereas the merit of the intramolecular FRET probe lies in the high signal-to-noise ratio. Although these GFP-based probes are powerful tools for the visualization of signal transduction cascades, numerous pitfalls remain associated with this technique. Here, we provide an overview of the GFP-based FRET probes and discuss these issues.