Inflammatory markers (IM) are elevated in atrial fibrillation (AF). However the relation of IM to substrate modification in AF remains unclear. We sought to assess the relationship of IM to fractionated atrial electrogram (FAE) in patients undergoing AF ablation. Methods: At baseline, left atrial (LA) pressure was recorded and blood was tested for IM. FAE mapping was performed before and after circumferential pulmonary vein and linear ablation (CPVA-L) and followed by FAE ablation. Image processing was used to define the FAE areas. AF cycle-length (AFCL) was compared between baseline and after ablations from left atrial electrode. Results: Older patients had higher cytokine levels. FAE area at baseline negatively correlated with the levels of interleukin-6 (IL-6, R=0.97 and p=0.03) and interleukin-12 (IL-12p70, R=0.97 and p=0.03). In addition, a significant reduction in FAE area and index occurred after CPVA-L (p=0.0001). FAE after CPVA-L correlated with left atrial pressure (LAP), [R² 0.5, (p=0.02)]. The AFCL (in msec) increased from 135 ± 41 to 149.5+30 (p=ns) after CPVA-L and further increased to 191.5 ± 60 (p=0.007) after FAE ablation. Conclusions: Older patients, known to have higher prevalence of AF, have elevated cytokine levels. There is a negative correlation of IL-6 and IL-12p70 to baseline FAE. FAE ablation performed after CPVA-L increases AFCL suggesting that these areas likely represent primary fractionation due to rotors. Sequestration of cytokines in the atrium could predispose to secondary fractionation, while primary fractionation noted after CPVA-L is related to LAP.