Cellular homeostasis requires precise communication between various types of organelles. In particular, the communication between nucleus and semiautonomous organelles, mitochondria and chloroplasts, has received widespread attention. Communication from nucleus to other organelles is known as anterograde signaling, whereas communication from mitochondria or chloroplasts to the nucleus is known as retrograde signaling. Here we discuss methods used to study retrograde signaling in Arabidopsis thaliana. These methods may also be modified to study retrograde signaling in other plant species.