A 3D atrial model was used to simulate the electrical activity of four different flutter propagation patterns: typical flutter, reverse typical flutter, superior vena cava flutter and inferior vena cava flutter. In this study we propose the use of the causal method to analyse the intracardiac atrial signal in order to automatically obtain the optimal target site for ablation. The causal method summarizes the electrical activity recorded by the electrograms in a single map, called recurrence map (RM). Three main regions can be identified in this map: (1) atrial tissue that does not belong to the re-entrant circuit, (2) atrial tissue belonging to the re-entrant circuit and (3) the thinnest path in the re-entrant circuit, with RM values of 0.03 ± 0.04, 0.41 ± 0.16 and 0.95 ± 0.05, respectively. The region with highest RM values corresponds to the optimal site for the ablation therapy. The results obtained with atrial models during flutter suggest that the proposed method allows the identification of target sites for ablation in patients with atrial flutter. This method may be useful in clinical practice to obtain atrial propagation patterns from patients with atypical atrial flutter circuits and identify the best target regions for ablation.