OBJECTIVE Cranial magnetic resonance imaging findings of patients considered to be cryptogenic stroke may be useful in determining the clinical and prognostic significance of arrhythmias, such as atrial premature beats and atrial run attacks, that are frequently encountered in rhythm Holter analysis. This study was conducted to investigate the relationship between short atrial runs and frequent premature atrial contractions detected in Holter monitors and infarct distributions in cranial magnetic resonance imaging of patients diagnosed with cryptogenic stroke. METHODS We enrolled the patients with acute ischemic stroke whose etiology were undetermined. We divided the patients in two groups according to diffusion-weighted magnetic resonance imaging as single or multiple vascular territory acute infarcts. The demographic, clinical, laboratory, echocardiographic, and rhythm Holter analyses were compared. RESULTS The study investigated 106 patients diagnosed with cryptogenic stroke. Acute cerebral infarctions were detected in 31% of the investigated patients in multiple territories and in 69% in a single territory. In multivariate logistic regression analysis, the total premature atrial contraction count (OR = 1.002, 95% CI: 1.001⁻1.004, p = 0.001) and short atrial run count (OR = 1.086, 95% CI: 1.021⁻1.155, p = 0.008) were found as independent variables that could distinguish between infarctions in a single or in multiple vascular territories. CONCLUSIONS Rhythm Holter monitoring of patients with infarcts detected in multiple vascular territories showed significantly higher premature atrial contractions and short atrial run attacks. More effort should be devoted to the identification of cardioembolic etiology in cryptogenic stroke patients with concurrent acute infarcts in the multiple vascular territories of the brain.