Atrial fibrillation (AF), especially asymptomatic cases, is often detected by medical checkups. We investigated the outcome of AF ablation in cases detected by medical checkups. We reviewed the data of 735 patients with AF (56 ± 10 years, paroxysmal: 441 patients) who underwent initial catheter ablation. All patients were divided into two groups based on their AF being diagnosed either by a medical checkup (group M) or not (group NM). AF was diagnosed by medical checkups in 263 (36%) patients. In Group M, the age was younger, time from the diagnosis to ablation shorter, left atrium dimension larger, and left ventricular ejection fraction lower than in Group NM. Male gender, persistent AF, and asymptomatic AF were more frequently seen in Group M than in Group NM. A mean of 13 ± 11 months after the initial ablation procedure, AF recurrence was more frequently observed in group M compared to group NM (P = 0.018). While the AF recurrence rate was similar in both groups in persistent AF patients (P = 0.87), it was more frequently observed in Group M than in Group NM in paroxysmal AF patients (P = 0.005). AF diagnosed by medical checkups was often associated with a worse outcome of catheter ablation, especially in paroxysmal AF patients.