The concept of dominant frequency (DF) has been used as a way to express local atrial activation rate during atrial fibrillation (AF). The rotor theory explaining the pathophysiology of AF is widely based upon spatial distribution of DF in the atria. Using frequency domain analysis to represent the rate of atrial activation by DF can avoid some of the limitations of time domain analysis of signals during AF. Understanding the concept of DF is of utmost importance to the proper use and interpretation of frequency domain analysis in AF. The current review focuses on the basic principles and methodology of frequency domain analysis using the Fourier transform during different types of AF. It also provides an update of the published experimental and clinical data on frequency domain analysis in light of the rotor theory for AF maintenance.