Background We previously reported that non-ischemic titrated cardiac injury by radiofrequency catheter ablation (RFCA) of atrial fibrillation (AF) mobilizes bone marrow derived CD34+ mononuclear cells. We hypothesized that degree of post-RFCA CD34+cell mobilization affects the clinical outcome of AF ablation. Methods Fifty-six patients (39 males, 53 짹 13 years) who underwent electrophysiology study (EPS; n = 10) or RFCA of AF (n = 46) were included. Peripheral blood CD34+ cell count and multiple serologic markers were evaluated before, immediately after the procedure. Results 1. The percent increase of CD34+ cells (%��CD34+) was significant after RFCA compared to EPS (60.2 짹 87.3 % vs. -26.3 짹 40.0 %, p<0.01), and correlated with RF duration (R = 0.40, p < 0.05) and plasma level of troponin I (R = 0.38, p < 0.001). 2. During 30 짹 2 months follow-up, AF recurred in 39 % of patients. The duration of RF energy delivery was longer (94.6 짹30.5 min vs. 77.2 짹 26.6 min, p < 0.05) and the proportion of persistent AF was higher (69 % vs. 30 %, p < 0.05) in patients with AF recurrence after RFCA. 3. In contrast, %��CD34+ was significantly lower in patients with recurrence than those remained in sinus rhythm (14.6 짹54.8 % vs. 70.5 짹 97.2 %, p < 0.05). Conclusion Although CD34+ mononuclear cells were mobilized after RFCA with dose dependent manner and AF recurrence rate was higher in patients with longer duration of RF energy delivery, %��CD34+ was lower in patients with recurrence than those remained in sinus rhythm after RFCA of AF. This finding suggests poor clinical outcome after AF ablation in patients with impaired mobilization of bone marrow derived CD34+ cells.