Complex fractionated atrial electrogram (CFAE) has been suggested to contribute to the maintenance of atrial fibrillation (AF). However, electrophysiologic characteristics of the left atrial myocardium responsible for genesis of CFAE have not been clarified. Non-contact mapping of the left atrium was performed at 37 AF onset episodes in 24 AF patients. Electrogram amplitude, width, and conduction velocity were measured during sinus rhythm, premature atrial contraction (PAC) with long- (L-PAC), short- (S-PAC) and very short-coupling intervals (VS-PAC). These parameters were compared between CFAE and non-CFAE regions. Unipolar electrogram amplitude was higher in CFAE than non-CFAE during sinus rhythm, L-, S- and VS-PAC (1.82 ± 0.73 vs. 1.13 ± 0.38, p < 0.001; 1.44 ± 0.54 vs. 0.92 ± 0.35, p < 0.001; 1.09 ± 0.40 vs. 0.70 ± 0.27, p < 0.001; 0.76 ± 0.30 vs. 0.53 ± 0.25 mV, p < 0.001). Laplacian bipolar electrogram amplitude was also higher in CFAE than non-CFAE during sinus rhythm, L-, S- and VS-PAC. Unipolar electrogram width was similar in CFAE and non-CFAE. Laplacian bipolar electrogram width was wider in CFAE than non-CFAE during L-, S- and VS-PAC (85.5 ± 6.8 vs. 79.6 ± 4.5, p < 0.001; 96.1 ± 9.7 vs. 84.5 ± 5.9, p < 0.001; 122.4 ± 16.0 vs. 99.6 ± 9.6 ms, p < 0.001), but not during sinus rhythm. The conduction velocity was slower in CFAE during sinus rhythm, L-, S- and VS-PAC than non-CFAE (1.7 ± 0.3 vs. 2.4 ± 0.4, p < 0.001; 1.4 ± 0.3 vs. 2.0 ± 0.5, p < 0.001; 1.2 ± 0.3 vs. 1.7 ± 0.5, p < 0.001; and 0.9 ± 0.3 vs. 1.4 ± 0.4 m/s, p < 0.001). CFAE was generated in the high amplitude atrial myocardium with slow and non-uniform conduction properties which were pronounced associated with premature activation, suggesting that heterogeneous conduction produced in high amplitude region contributes to the genesis of CFAE.