The complex fractioned atrial electrogram (CFAE) has been considered as the catheter ablation target of left atrium (LA) under persistent atrial fibrillation (PeAF). We evaluated the relation between the LA wall composition by late gadolinium enhancement cardiac magnetic resonance (LGE-CMR) and the CFAE in patients with PeAF. Forty-three patients underwent LGE-CMR and CFAE mapping before catheter ablation for PeAF. The LA wall substrates were classified into three: the fibrotic, intermediate, and normal substrates by using two thresholds of 2 standard deviation (2-SD) and 6-SD above the mean signal from the normal myocardium. For each of 12 preselected LA wall regions, the composition ratios (CRs) of fibrotic, indeterminate, and normal substrates were calculated as a percentage to the volume of LA wall region, and compared depending on the CFAE, respectively. The CR of normal substrate was significantly greater at the LA wall region with CFAE (52 ± 38% vs. 20 ± 28%, P < 0.01) than without CFAE. In contrast, the LA wall region with CFAE showed significantly lower CRs of intermediate substrate (39 ± 34% vs. 57 ± 31%, P < 0.01) and fibrotic substrate (7 ± 17% vs. 21 ± 24%, P < 0.01) than did the LA wall region without CFAE, respectively. Thus, the high CR (>18%) of normal substrate predicted the CFAE at the corresponding LA wall region with 71% sensitivity and 62% specificity. In conclusion, the evaluation of LA wall normal substrate by LGE-CMR might be useful to predict the CFAE occurrence before catheter ablation of PeAF.