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Mice are routinely used to investigate molecular mechanisms underlying the atrial fibrillation (AF) substrate. We sought to optimize transesophageal rapid atrial pacing (RAP) protocols for the detection of AF susceptibility in mouse models. Hypertensive and control C57Bl/6J mice were subjected to burst RAP at a fixed stimulus amplitude. The role of parasympathetic involvement in pacing-related atrioventricular (AV) block and AF was examined using an intraperitoneal injection of atropine. In a crossover study, burst and decremental RAP at twice diastolic threshold were compared for induction of AV block during pacing. The efficacy of burst and decremental RAP to elicit an AF phenotype was subsequently investigated in mice deficient in the lymphocyte adaptor protein ( Lnk -/- ) resulting in systemic inflammation, or the paired-like homeodomain-2 transcription factor ( Pitx2 +/- ) as a positive control. When pacing at a fixed stimulus intensity, pacing-induced AV block with AF induction occurred frequently, so that there was no difference in AF burden between hypertensive and control mice. These effects were prevented by atropine administration, implicating parasympathetic activation due to ganglionic stimulation as the etiology. When mice with AV block during pacing were eliminated from the analysis, male Lnk -/- mice displayed an AF phenotype only during burst RAP compared with controls, whereas male Pitx2 +/- mice showed AF susceptibility during burst and decremental RAP. Notably, Lnk -/- and Pitx2 +/- females exhibited no AF phenotype. Our data support the conclusion that multiple parameters should be used to ascertain AF inducibility and facilitate reproducibility across models and studies. NEW & NOTEWORTHY Methods were developed to optimize transesophageal rapid atrial pacing (RAP) to detect AF susceptibility in new and established mouse models. High stimulus intensity and pacing rates caused parasympathetic stimulation, with pacing-induced AV block and excessive AF induction in normal mice. For a given model, pacing at twice TH enabled improved phenotype discrimination in a pacing mode and sex-specific manner. Transesophageal RAP should be individually optimized when developing a mouse model of AF.