A relevant part of embolic strokes of undetermined source (ESUS) is assumed to be cardiogenic. As shown previously, certain biomarkers of endothelial pathology are related to atrial fibrillation (AF). In this long-term follow-up study, we aimed to investigate whether these biomarkers are associated with subsequently diagnosed AF and with atrial cardiopathy. In 98 patients who suffered ischemic stroke of known and unknown origin L-arginine, Asymmetric (ADMA) and Symmetric Dimethylarginine (SDMA) have been measured on follow-up at least one year after index stroke. Stroke-diagnostics were available for all patients, including carotid Intima-Media-Thickness (CIMT) and comprehensive echocardiography studies. CIMT was larger in AF- compared with ESUS-patients (P < 0.001), independently from CHA2DS2VASC in the regression analysis (P = 0.004). SDMA-values were stable over time (P < 0.001; r = 0.788), whereas for ADMA moderate correlation with the initial values could be found (P = 0.007; r = 0.356). According to Kaplan-Meier-analyses, AF-detection rates were associated with CIMT (P = 0.003) and SDMA (P < 0.001). SDMA correlated with left atrial volume-index within the whole collective (P = 0.003, r = 0.322) and within the ESUS-subgroup (P = 0.003; r = 0.446). These associations were independent from CHA2DS2VASC and renal function in the regression analysis (P = 0.02 and P = 0.005, respectively). In conclusion, these results highlight SDMA and CIMT as potential markers of atrial cardiopathy and AF in ESUS-patients.