Background-The mechanisms underlying the transition of typical atrial flutter (Afl) to fibrillation (AF) remain unclear.We set out to test the hypothesis that Afl disorganizes to AF via alternans of atrial action potentials. Methods and Results-In 38 patients with Afl, monophasic action potentials (MAPs) were recorded at the isthmus and either high or low right atrium (HRA, LRA) during overdrive pacing to 160 ms or to the initiation of AF, whichever came first. MAP duration measured at 90% repolarization was longer at the isthmus in all patients, and failed to shorten with rate, compared with the HRA (nϭ38) or LRA (nϭ5). In 20 patients who developed AF, progressive pacing first caused alternans of isthmus MAP duration and amplitude at mean cycle length of 219Ϯ45 ms, followed by AF at a mean onset cycle length of 184Ϯ38 ms. Subsets of this group showed spontaneous action potential duration alternans at the isthmus (11 of 20 patients) and 2:1 isthmus conduction block immediately preceding AF (4 of 20 patients). In the 18 patients who did not develop AF, MAP alternans was less common (9 of 18 patients; PϽ0.0003), and occurred only at faster pacing (cycle lengthϭ169Ϯ25 ms; PϽ0.05). Conclusions-In patients with typical Afl, action potential duration rate maladaptation at the isthmus may lead to action potential duration alternans and conduction block preceding the transition to AF. These isthmus characteristics may enable the spontaneous initiation of AF through wavefront fractionation and may explain the benefits of isthmus ablation in preventing AF recurrence.