The invention relates to a method and system for detecting atrial arrhythmia, especially atrial fibrillations. Based on at least one electrical signal indicative of a heart's activity, a plurality of short-term HRV data sets are generated, one short-term HRV data set indicating the heart's rate variability within a time period of a given length, and two consecutive short-term HRV data sets having a given time difference. A frequency analysis of each short-term HRV data set is then performed and a power level corresponding to at least one selected frequency component in each short-term HRV data set is defined. The occurrence of the heart's atrial arrhythmia episodes are then estimated on the basis of the power levels defined.