Helicobacter pylori virulent strains have been shown to affect cardiovascular diseases through molecular mimicry mechanisms. Silent autoimmune myocarditis has been hypothesized to be the cause of idiopathic dysrhythmias (IA). The aim of this study is to assess the prevalence of virulent H. pylori strains in patients affected by IA. In this study,54 patients (40 men, mean age 44 ± 17 years) affected by IA and 50 healthy subjects (34 men, mean age 45 ± 9) were evaluated. IA, defined as dysrhythmias with no evidence of other cardiac pathology, were either supraventricular (SVA, 23 patients; mean age 45 ± 15 years) or ventricular (VA, 31 patients; mean age 42 ± 18 years). H. pylori infection and gastrointestinal (GI) symptoms were evaluated. H. pylori strains expressing the cytotoxin-associated gene A (cagA) and the vacuolating-cytotoxin A (vacA) were also assessed through western blot. The prevalence of H. pylori is similar in IA patients and in controls (42 vs. 44%; p > 0.05); H. pylori infection is observed in 48 and 39% of the patients are affected by SVA and VA, respectively. The prevalence of CagA-positive strains is increased in IA patients compared to controls (65 vs. 42%; p < 0.01); similarly, the prevalence of VacA-positive strains is also increased in IA patients (74 vs. 46%; p < 0.006). Excluding belching, infected patients did not show any difference in GI symptoms, when compared to non-infected subjects. From this study it is concluded that there is an epidemiological link between CagA and VacA-positive H. pylori strains in IA patients.