Background There is limited data regarding effect of prolonged radiation exposure during electrophysiological (EP) procedures on direct DNA damage. Comet test has shown to assess DNA damage following radiation exposure. Methods We performed a single-center prospective observational study assessing direct DNA damage using the quantitative comet assay in patients undergoing cardiac resynchronization (CRT) and atrial fibrillation (AF) catheter ablation procedures. Venous comet assay was performed pre, immediately post procedure and at 3-month duration in twenty-two (N=22) patients who underwent catheter ablation for symptomatic AF and fourteen (N=14) patients who underwent CRT implantation. Results The median [interquartile range (IQR)] fluoroscopy time, radiation dose and dose area product (DAP) were 34.3 (27.97 – 45.48) minutes, 853.07 (611.36 - 1334.76) mGy and 16,994.10 (9,023.65 – 58,845.00) UGym2 in the ablation group and 30.05 (18.75 - 37.33) minutes, 345.00 (165.09 - 924.79) mGy and 11,837.20 [7182.67 - 35567.75] UGym2 in the CRT group. When compared with pre-procedure, there was a statistically significant increase in median (IQR) DNA migration on comet assay in the ablation group immediately post procedure [+6.55 µm (0.78, 10.25, p=0.02)] that subsequently decreased at 3 months [-1.00 µm (-2.20, 0.78), p=0.03] but not in the CRT group. Conclusion There was a significant increase in DNA damage as detected by comet assay immediately post procedure that normalized at 3 months in patients undergoing AF ablation. Further large prospective studies are warranted to evaluate the impact of this prolonged radiation exposure and DNA damage on long-term follow up.