Purpose We aimed to define the role of extended pulmonary vein isolation (PVI), posterior wall isolation, and mitral isthmus lines to eliminate electrograms exhibiting fractionation pattern during stepwise ablation on acute atrial fibrillation (AF) termination rate in patients with long-standing persistent AF (LSPAF). Methods Twelve patients with LSPAF underwent ablation during AF. Using the fractionation mapping tool of the Ensite (TM) (Abbott Medical, Chicago, USA) system, sites exhibiting discrete atrial complexes and consistent activation sequence were mapped. The areas with a fractionation score above 4 were accepted as potential drivers for AF. During stepwise ablation consisting of circumferential PVI, roof and floor lines for posterior wall isolation, and mitral isthmus lines, ablation lines were extended toward potential AF drivers on the fractionation map as much as possible until sinus was achieved by ablation. Results Fractionation-guided ablation caused acute AF termination in 8 of 12 patients. In 6 of 12 cases, AF returned to sinus rhythm during the extended ablation. In 2 patients, AF shifted to sinus after cavotricuspid isthmus ablation. Sinus was achieved by cardioversion in 3 of cases. Procedural failure was seen in one case with significant scar tissue. During a mean follow-up of 31.5 +/- 11 months, overall arrhythmia-free survival was 92% with 2 procedures. Conclusions This pilot study demonstrates that fractionation mapping-guided ablation may provide an adjunctive benefit in terms of acute AF termination in patients with LSPAF. These results should be confirmed by larger, randomized, comparison studies between linear ablation and extended ablation without elimination of electrograms (EGMs) with fractionation.